The Second Messenger Cyclic Di-GMP

357 Pages·2010·8.575 MB·English

by  Visick, Karen L., Wolfe, Alan J

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Library of Congress Cataloging-in-Publication Data
The second messenger cyclic di-GMP / edited by Alan J. Wolfe and Karen L. Visick.
p. ; cm.
Includes bibliographical references and index.
ISBN 978-1-55581-499-1 (hard cover)
1. Cyclic guanylic acid. 2. Second messengers (Biochemistry) I. Wolfe, Alan J. II. Visick, Karen L.
III. American Society for Microbiology.
[DNLM: 1. Cyclic GMP—physiology. 2. Bacterial Physiological Phenomena. 3. Cyclic GMP—analogs &
derivatives. 4. Genome, Bacterial. 5. Signal Transduction—physiology. QU 58 S445 2010]
QP625.N89S43 2010
572.8’6293—dc22
2009036432
Current printing (last digit)
10 9 8 7 6 5 4 3 2 1
All Rights Reserved
Printed in the United States of America
Coverillustration:AwrinkledcolonyformedbyamutantofVibriocholerae.Thephenotypeisassociatedwith
cyclic di-GMP production. (Courtesy of Nicholas J. Shikuma and Fitnat H. Yildiz.)
CONTENTS
Contributors • vii 7. Making, Breaking, and Sensing of Cyclic
Preface • xi Di-GMP: Structural, Thermodynamic, and
Evolutionary Principles • 76
Dorothy Kim, John F. Hunt, and Tilman Schirmer
I. Second Messengers: an Overview
III. Cyclic Di-GMP and Lifestyle Choices
1. Introduction to Second Messengers: Lessons
from Cyclic AMP • 3
8. Choosing the Right Lifestyle: Regulation
Alan J. Wolfe
of Developmental Pathways by Cyclic
Di-GMP • 99
Matthew Parsek and Phillip Aldridge
II. General Principles: the Core
9. Role of Cyclic Di-GMP in Caulobacter
2. Moshe Benziman and the Discovery of Cyclic crescentus Development and Cell Cycle
Di-GMP • 11 Control • 120
Dorit Amikam, Haim Weinhouse, and Michael Y. So¨ren Abel and Urs Jenal
Galperin
10. Hierarchical Control of rdar Morphotype
3. Ubiquity of Cyclic Di-GMP Pathways: a Development of Salmonella enterica by Cyclic
Bioinformatic Analysis • 24 Di-GMP • 137
Michael Y. Galperin Ute Ro¨mling, Kristina Jonas, O¨jar Melefors, Nina
Grantcharova, and Agaristi Lamprokostopoulou
4. The Core Pathway: Diguanylate Cyclases,
Cyclic Di-GMP-Specific Phosphodiesterases, and 11. Role of Cyclic Di-GMP in Pseudomonas
Cyclic Di-GMP-Binding Proteins • 37 aeruginosa Biofilm Development • 156
Mark Gomelsky Caroline S. Harwood
5. The HD-GYP Domain and Cyclic Di-GMP 12. The Scr Circuit in Vibrio parahaemolyticus
Signaling • 57 Modulates Swarming and Sticking • 173
Robert P. Ryan, Yvonne McCarthy, and J. Maxwell Linda L. McCarter
Dow
13. Roles of Diguanylate Cyclases and
6. Methods for Cyclic Di-GMP Phosphodiesterases in Motility and Biofilm
Detection • 68 Formation in Vibrio fischeri • 186
Christopher M. Waters Alan J. Wolfe and Karen L. Visick
v
vi CONTENTS
14. Csr (Rsm) System and Its Overlap and IV. Cyclic Di-GMP, Pathogenesis, and Host
Interplay with Cyclic Di-GMP Regulatory Immunity
Systems • 201
Tony Romeo and Paul Babitzke
20. Role of Cyclic Di-GMP in Vibrio cholerae
Virulence • 293
15. Riboswitches That Sense Cyclic
Di-GMP • 215 Jason T. Pratt, Rita Tamayo, and Andrew Camilli
Elaine R. Lee, Narasimhan Sudarsan, and Ronald R.
Breaker 21. Cyclic Di-GMP Signaling and Host
Immunity • 304
16. Role of Cyclic Di-GMP in the Regulatory David K. R. Karaolis and Theodore J. Standiford
Networks of Escherichia coli • 230
Regine Hengge 22. Bis-(3(cid:2),5(cid:2))-Cyclic Di-GMP: Promising
Adjuvant for Vaccine Design • 311
17. Cyclic Di-GMP Signaling in Vibrio Thomas Ebensen, Rimma Libanova, and Carlos A.
cholerae • 253 Guzm´an
Sinem Beyhan and Fitnat H. Yildiz
18. Role of Cyclic Di-GMP in Biofilm V. Conclusions
Development and Signaling in Yersinia
pestis • 270
23. Cyclic Di-GMP: Using the Past To Peer into
Robert D. Perry and Alexander G. Bobrov
the Future • 323
Karen L. Visick and Alan J. Wolfe
19. Environmental Control of Cyclic Di-GMP
Signaling in Pseudomonas fluorescens: from Signal
to Output • 282
Peter D. Newell and George A. O’Toole Index • 333
CONTRIBUTORS
So¨ren Abel J. Maxwell Dow
Biozentrum, University of Basel, CH-4056 Basel, BIOMERIT Research Centre, Department of
Switzerland Microbiology, BioSciences Institute, University
College Cork, Cork, Ireland
Phillip Aldridge
Centre for Bacterial Cell Biology and Institute for Thomas Ebensen
Cell and Molecular Biosciences, Newcastle Department of Vaccinology and Applied
University, Newcastle upon Tyne, NE2 4HH, Microbiology, Helmholtz Centre for Infection
United Kingdom Research, 38124 Braunschweig, Germany
Dorit Amikam Michael Y. Galperin
P.O. Box 10356, Zichron Yakov 30900, Israel National Center for Biotechnology Information,
National Library of Medicine, National Institutes of
Health, Bethesda, MD 20894
Paul Babitzke
Department of Biochemistry and Molecular
Mark Gomelsky
Biology, The Pennsylvania State University,
Department of Molecular Biology, University of
University Park, PA 16802
Wyoming, Laramie, WY 82071
Sinem Beyhan
Nina Grantcharova
Department of Microbiology and Environmental
Department of Microbiology, Tumor and Cell
Toxicology, University of California, Santa Cruz,
Biology, Karolinska Institutet, SE-171 77
Santa Cruz, CA 95064
Stockholm, Sweden
Alexander G. Bobrov
Carlos A. Guzma´n
Department of Microbiology, Immunology, and
Department of Vaccinology and Applied
Molecular Genetics, University of Kentucky,
Microbiology, Helmholtz Centre for Infection
Lexington, KY 40536-0298
Research, 38124 Braunschweig, Germany
Ronald R. Breaker
Caroline S. Harwood
Department of Molecular, Cellular and
Department of Microbiology, The University of
Developmental Biology, Department of Molecular Washington, Seattle, WA 98195
Biophysics and Biochemistry, and Howard Hughes
Medical Institute, Yale University, New Haven, CT Regine Hengge
06520 Institut fu¨r Biologie—Mikrobiologie, Freie
Universit¨at Berlin, 14195 Berlin, Germany
Andrew Camilli
Howard Hughes Medical Institute and Department John F. Hunt
of Molecular Biology and Microbiology, Tufts Department of Biological Sciences, Columbia
University School of Medicine, Boston, MA 02111 University, New York, NY 10027
vii
viii CONTRIBUTORS
Urs Jenal Matthew Parsek
Biozentrum, University of Basel, CH-4056 Basel, Department of Microbiology, University of
Switzerland Washington, School of Medicine, Seattle, WA
98195-7242
Kristina Jonas
Department of Microbiology, Tumor and Cell
Robert D. Perry
Biology, Karolinska Institutet, SE-171 77
Department of Microbiology, Immunology, and
Stockholm, Sweden
Molecular Genetics, University of Kentucky,
Lexington, KY 40536-0298
David K. R. Karaolis
Intragenics Research Institute, Havre de Grace, MD
Jason T. Pratt
21078, and Karagen Pharmaceuticals, Baltimore,
Howard Hughes Medical Institute and Department
MD 21210
of Molecular Biology and Microbiology, Tufts
University School of Medicine, Boston, MA 02111
Dorothy Kim
Department of Biological Sciences, Columbia
University, New York, NY 10027 Tony Romeo
Department of Microbiology and Cell Science,
Agaristi Lamprokostopoulou University of Florida, Gainesville, FL 32611
Department of Microbiology, Tumor and Cell
Biology, Karolinska Institutet, SE-171 77 Ute Ro¨mling
Stockholm, Sweden Department of Microbiology, Tumor and Cell
Biology, Karolinska Institutet, SE-171 77
Elaine R. Lee Stockholm, Sweden
Department of Molecular, Cellular and
Developmental Biology, Yale University, New
Robert P. Ryan
Haven, CT 06520
BIOMERIT Research Centre, Department of
Microbiology, BioSciences Institute, University
Rimma Libanova
College Cork, Cork, Ireland
Department of Vaccinology and Applied
Microbiology, Helmholtz Centre for Infection
Tilman Schirmer
Research, 38124 Braunschweig, Germany
Core Program Structural Biology and Biophysics,
Biozentrum, University of Basel, CH-4056, Basel,
Linda L. McCarter
Department of Microbiology, The University of Switzerland
Iowa, Iowa City, IA 52242
Theodore J. Standiford
Yvonne McCarthy Department of Internal Medicine, Division of
BIOMERIT Research Centre, Department of Pulmonary and Critical Care Medicine, University
Microbiology, BioSciences Institute, University of Michigan Medical Center, Ann Arbor, MI 48109
College Cork, Cork, Ireland
Narasimhan Sudarsan
O¨jar Melefors
Howard Hughes Medical Institute, Yale University,
Department of Microbiology, Tumor and Cell
New Haven, CT 06520
Biology, Karolinska Institutet, SE-171 77
Stockholm, Sweden
Rita Tamayo
Department of Microbiology and Immunology, The
Peter D. Newell
University of North Carolina at Chapel Hill, Chapel
Department of Microbiology and Immunology,
Hill, NC 27599
Dartmouth Medical School, Hanover, NH 03755
George A. O’Toole Karen L. Visick
Department of Microbiology and Immunology, Department of Microbiology and Immunology,
Dartmouth Medical School, Hanover, NH 03755 Loyola University Chicago, Maywood, IL 60153
CONTRIBUTORS ix
Christopher M. Waters Alan J. Wolfe
Department of Microbiology and Molecular Department of Microbiology and Immunology,
Genetics, Michigan State University, East Lansing, Loyola University Chicago, Maywood, IL 60153
MI 48824
Haim Weinhouse Fitnat H. Yildiz
Department of Biological Chemistry, The Alexander Department of Microbiology and Environmental
Silberman Institute for Life Sciences, Hebrew Toxicology, University of California, Santa Cruz,
University of Jerusalem, Jerusalem 91904, Israel Santa Cruz, CA 95064