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Gene and Protein Evolution
Genome Dynamics Vol. 3
Series Editor
Jean-Nicolas Volff, Lyon Executive Editor
Michael Schmid, Würzburg Advisory Board
John F.Y. Brookfield, Nottingham Jürgen Brosius, Münster Pierre Capy, Gif-sur-Yvette Brian Charlesworth, Edinburgh Bernard Decaris, Vandoeuvre-lès-Nancy Evan Eichler, Seattle, WA John McDonald, Atlanta, GA Axel Meyer, Konstanz Manfred Schartl, Würzburg
Gene and Protein Evolution
Volume Editor
Jean-Nicolas Volff, Lyon
34 figures, 18 in color, and 10 tables, 2007
Basel · Freiburg · Paris · London · New York · Bangalore · Bangkok · Singapore · Tokyo · Sydney
Prof. Jean-Nicolas Volff Institut de Génomique Fonctionnelle de Lyon Ecole Normale Supérieure de Lyon 46 allée d’Italie F-69364 Lyon Cedex 07 (France)
Library of Congress Cataloging-in-Publication Data Gene and protein evolution / volume editor, Jean-Nicolas Volff. p. ; cm. – (Genome dynamics, ISSN 1660-9263 ; v. 3) Includes bibliographical references and indexes. ISBN-13: 978-3-8055-8340-4 (hard cover : alk. paper) 1. Genomics. 2. Molecular evolution. 3. Proteins–Evolution. I. Volff, Jean-Nicolas. II. Series. [DNLM: 1. Genomics. 2. Evolution, Molecular. 3. Proteins. QU 58.5 G3255 2007] QH447.G44 2007 572.8⬘38–dc22 2007024911
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Contents
VII Preface 1 Coevolution within and between Genes Galtier, N.; Dutheil, J. (Montpellier)
13 Evolution of Protein-Protein Interaction Network Makino, T. (Mishima/Shizuoka/Dublin); Gojobori, T. (Mishima/Tokyo)
30 Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity Pallen, M.J. (Birmingham); Gophna, U. (Tel-Aviv)
48 Comparative Genomics and Evolutionary Trajectories of Viral ATP Dependent DNA-Packaging Systems Burroughs, A.M. (Bethesda, Md./Boston, Mass.); Iyer, L.M.; Aravind, L. (Bethesda, Md.)
66 General Trends in the Evolution of Prokaryotic Transcriptional Regulatory Networks Madan Babu, M. (Bethesda, Md./Cambridge); Balaji, S.; Ara