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[email protected] Online: estore.asm.org Copyright 2010 ASM Press American Society for Microbiology 1752 N St. NW Washington, DC 20036-2904 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 Cover illustration: A wrinkled colony formed by a mutant of Vibrio cholerae. The phenotype is associated with cyclic di-GMP production. (Courtesy of Nicholas J. Shikuma and Fitnat H. Yildiz.) CONTENTS Contributors Preface • I. • xi 7. Making, Breaking, and Sensing of Cyclic Di-GMP: Structural, Thermodynamic, and Evolutionary Principles • 76 Dorothy Kim, John F. Hunt, and Tilman Schirmer vii Second Messengers: an Overview III. 1. Introduction to Second Messengers: Lessons from Cyclic AMP • 3 Alan J. Wolfe II. Cyclic Di-GMP and Lifestyle Choices 8. Choosing the Right Lifestyle: Regulation of Developmental Pathways by Cyclic Di-GMP • 99 Matthew Parsek and Phillip Aldridge General Principles: the Core 9. Role of Cyclic Di-GMP in Caulobacter crescentus Development and Cell Cycle Control • 120 So ¨ren Abel and Urs Jenal 2. Moshe Benziman and the Discovery of Cyclic Di-GMP • 11 Dorit Amikam, Haim Weinhouse, and Michael Y. Galperin 10. Hierarchical Control of rdar Morphotype Development of Salmonella enterica by Cyclic Di-GMP • 137 ¨ jar Melefors, Nina Ute Ro ¨mling, Kristina Jonas, O Grantcharova, and Agaristi Lamprokostopoulou 3. Ubiquity of Cyclic Di-GMP Pathways: a Bioinformatic Analysis • 24 Michael Y. Galperin 4. The Core Pathway: Diguanylate Cyclases, Cyclic Di-GMP-Specific Phosphodiesterases, and Cyclic Di-GMP-Binding Proteins • 37 Mark Gomelsky 11. Role of Cyclic Di-GMP in Pseudomonas aeruginosa Biofilm Development • 156 Caroline S. Harwood 5. The HD-GYP Domain and Cyclic Di-GMP Signaling • 57 Robert P. Ryan, Yvonne McCarthy, and J. Maxwell Dow 12. The Scr Circuit in Vibrio parahaemolyticus Modulates Swarming and Sticking • 173 Linda L. McCarter 13. Roles of Diguan