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Genetics and Regulation of Nitrogen Fixation in Free-Living Bacteria Nitrogen Fixation: Origins, Applications, and Research Progress

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Genetics and Regulation of Nitrogen Fixation in Free-Living Bacteria Nitrogen Fixation: Origins, Applications, and Research Progress Genetics and Regulation of Nitrogen Fixation in Free-Living Bacteria Nitrogen Fixation: Origins, Applications, and Research Progress VOLUME 2 Genetics and Regulation of Nitrogen Fixation in Free-Living Bacteria Edited by Werner Klipp Lehrstuhl für Biologie der Mikroorganismen, Fakultät für Biologie, Ruhr-Universität Bochum, Germany Bernd Masepohl Lehrstuhl für Biologie der Mikroorganismen, Fakultät für Biologie, Ruhr-Universität Bochum, Germany John R. Gallon Biochemistry Research Group, School of Biological Sciences, University of Wales, Swansea, U.K. and William E. Newton Department of Biochemistry, Virginia Polytechnic Institute & State University, Blacksburg, U.S.A. KLUWER ACADEMIC PUBLISHERS NEW YORK, BOSTON, DORDRECHT, LONDON, MOSCOW eBook ISBN: 1-4020-2179-8 Print ISBN: 1-4020-2178-X ©2005 Springer Science + Business Media, Inc. Print ©2004 Kluwer Academic Publishers Dordrecht All rights reserved No part of this eBook may be reproduced or transmitted in any form or by any means, electronic, mechanical, recording, or otherwise, without written consent from the Publisher Created in the United States of America Visit Springer's eBookstore at: http://ebooks.kluweronline.com and the Springer Global Website Online at: http://www.springeronline.com v TABLE OF CONTENTS Series Preface . ix Preface. xiii List of Contributors. xvii Dedication – Werner Klipp and John Gallon. xix Chapter 1. Historical Perspective – Development of nif Genetics and Regulation in Klebsiella pneumoniae R. Dixon . 1 1. Introduction . 1 2. The Early Years . 2 3. Defining the K. pneumoniae nif Genes . 4 4. The Recombinant DNA Era . 5 5. nif Gene Regulation . 6 6. Coda . 16 References . 17 Chapter 2. Genetics of Nitrogen Fixation and Related Aspects of Metabolism in Species of Azotobacter: History and Current Status C. Kennedy and P. Bishop . 27 1. Research on the Genus Azotobacter (1901-2003) . 27 2. Application of the Tools of Genetics and Molecular Biology in Species of Azotobacter . 29 3. The nif Genes encoding the Enzymes for Structure, Function, and Biosynthesis of Mo-containing Nitrogenase . 33 4. Regulation of Expression of nif and Associated Genes by Ammonium and O2 . 35 5. Ancillary Properties of Azotobacter Species that Aid the Efficiency of Nitrogen Fixation . 36 6. Discovery of Molybdenum-independent Nitrogenase Systems in A. vinelandii . 38 7. Molybdenum-independent Nitrogenase systems in other Azotobacter Species . 44 Acknowledgements . 45 References . 46 Chapter 3. Nitrogen Fixation in the Clostridia J.-S. Chen . 53 1. Introduction . 53 2. The Nitrogen-fixing Clostridia . 54 3. Distinctive Features of the nif Genes of the Clostridia . 55 vi 4. Genes for Ammonia Assimilation . 58 5. Regulation of Nitrogen Fixation and Ammonia Assimilation . 59 6. Concluding Remarks . 62 References . 62 Chapter 4. Regulation of Nitrogen Fixation in Methanogenic Archaea J. A. Leigh . 65 1. Introduction . 65 2. History and Background . 65 3. Transcriptional Regulation . 66 4. Regulation of Nitrogenase Activity . 69 5. Summary . 70 References . 71 Chapter 5. Nitrogen Fixation in Heterocyst-Forming Cyanobacteria T. Thiel . 73 1. Introduction . 73 2. Structure of Heterocysts . 74 3. Nitrogenase Genes . 78 4. Heterocyst Metabolism . 81 5. Genes Important for Heterocyst Formation . 88 6. Heterocyst Pattern Formation . 95 7. Regulation . 98 Acknowledgements . 101 References . 101 Chapter 6. N2 Fixation by Non-Heterocystous Cyanobacteria J. R. Gallon . 111 1. Introduction . 111 2. Non-heterocystous Cyanobacteria . 113 3. Patterns of N2 Fixation . 126 Acknowledgements . 133 References . 133 Chapter 7. Nitrogen Fixation in the Photosynthetic Purple Bacterium Rhodobacter capsulatus B. Masepohl, T. Drepper and W. Klipp . 141 1. Introduction . 141 2. Organization of Nitrogen-fixing Genes . 142 3. The Nitrogen-fixation Regulon of R. capsulatus . 155 4. Ammonium Control of Synthesis and Activity of both Nitrogenases . 158 5. Environmental Factors Controlling Nitrogen Fixation . 161 6. Linkage of Nitrogen Fixation, Photosynthesis, and Carbon Dioxide Assimilation . 162 7. Nitrogen Fixation in other Photosynthetic Purple Bacteria . 163 References . 165 vii Chapter 8. Post-translational Regulation of Nitrogenase in Photosynthetic Bacteria S. Nordlund and P. W. Ludden . 175 1. Introduction . 175 2. Discovery of Nitrogen Fixation by Photosynthetic Bacteria . 176 3. In vitro Studies of Nitrogenase in Photosynthetic Bacteria . 177 4. The Protein Era . 178 5. Evidence for the Drat/Drag System in other Organisms . 182 6. Other ADP-Ribosylations . 183 7. Genetics of the Drag/Drat System . 185 8. Signal Transduction to Drat and Drat . 185 9. Conclusions . 189 Acknowledgement . 190 References . 190 Chapter 9. Regulation of Nitrogen Fixation in Free-Living Diazotrophs M. J. Merrick . 197 1. Introduction . 197 2. General Nitrogen Control Systems . 198 3. nif-specific Nitrogen Control . 204 4. Nitrogen Control of Nitrogenase Activity . 211 5. Conclusions . 214 References . 215 Chapter 10. Molybdenum Uptake and Homeostasis R. N. Pau . 225 1. Molybdenum Outside Cells . 225 2. Transport . 230 3. Cytoplasmic Molybdate-binding Proteins . 236 4. The ATP-binding Protein of the Molybdate Transporter . 242 5. The Regulatory Protein, ModE . 243 6. Conclusions . 249 Acknowledgements . ..
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