Genomes and Genomics of Nitrogen-fixing Organisms This is Volume 3 of a seven-volume series on all aspects of Nitrogen Fixation. The series aims to be the definitive authority in the field and to act as a benchmark for some years to come. Rather than attempting to cram the whole field into a single volume, the subject matter is divided among seven volumes to allow authors the luxury of writing in depth with a comprehensive reference base. All authors are recognized practicing scientists in the area of their contribution, which ensures the high quality, relevance, and readability of the chapters. In establishing the rationale for, and the organization of, this book, we realized the need to divide it into two sections. The first section should be organism based and should review our current knowledge of the genomes of nitrogen-fixing organisms and what these nucleotide sequences tell us. The second section should then be technology based. It should review what technologies are available to mine the data inherent in the nucleotide sequences and how they are now being used to produce gene-function data from differential gene expression.

Inhalt

Preface to the Series. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii

List of Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xv

Chapter 1. Origins of Genomics in Nitrogen-Fixation Research

G. Dávila and R. Palacios . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

2. Symbiotic Organisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

3. Free-Living Organism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

4. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

   References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

   Chapter 2. Genomics of Diazotrophic Archaea

   J. A. Leigh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

5. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

6. The Core nif-gene Cluster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

7. Other nif Genes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

8. Other Nitrogen Assimilatory Genes . . . . . . . . . . . . . . . . . . . . . . . . . . 9

9. PII Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

   References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

   Chapter 3. GenomicAspects of Nitrogen Fixation in the Clostridia

   J.-S. Chen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

10. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

11. The Nitrogen-Fixing Clostridia. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

12. The Genome of the Clostridia. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

13. Organization of the Nitrogen-Fixation Gene Cluster . . . . . . . . . . . . 17

14. Regulatory Genes for Nitrogen Metabolism . . . . . . . . . . . . . . . . . . . 21

15. Altenative Nitrogen-Fixation (anf) Genes . . . . . . . . . . . . . . . . . . . . 23

16. Genes for Nitrogen Assimilation . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

17. Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

    References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

    Chapter 4. The Genome of the Filamentous Cyanobacterium Nostoc punctiforme

    J. C. Meeks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

18. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

19. Phenotypic Traits of N. punctiforme . . . . . . . . . . . . . . . . . . . . . . . . 29

20. Overview of the N. punctiforme Genome . . . . . . . . . . . . . . . . . . . . 37

21. N. punctiforme genes Involved in Heterocyst Formation, Nitrogenase

    Expression, and Ammonia and Nitrate Assimilation . . . . . . . . . . 46

22. Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

    Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

    References . . .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

    Chapter 5. The nif Genes of Rhodobacter capsulatus, Rhodobacter

    sphaeroides and Rhodopseudomonas palustris

    R. Haselkorn and V. Kapatral . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

23. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

    2. Regulation of the Nitrogen-Fixation System . . . . . . . . . . . ....