Biological Nitrogen Fixation E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 4127

Veröffentlichungsjahr: 2015

Beschreibung

Nitrogen is arguably the most important nutrient required by plants. However, the availability of nitrogen is limited in many soils and although the earth's atmosphere consists of 78.1% nitrogen gas (N2) plants are unable to use this form of nitrogen. To compensate , modern agriculture has been highly reliant on industrial nitrogen fertilizers to achieve maximum crop productivity. However, a great deal of fossil fuel is required for the production and delivery of nitrogen fertilizer. Moreover carbon dioxide (CO2) which is released during fossil fuel combustion contributes to the greenhouse effect and run off of nitrate leads to eutrophication of the waterways. Biological nitrogen fixation is an alternative to nitrogen fertilizer. It is carried out by prokaryotes using an enzyme complex called nitrogenase and results in atmospheric N2 being reduced into a form of nitrogen diazotrophic organisms and plants are able to use (ammonia). It is this process and its major players which will be discussed in this book. Biological Nitrogen Fixation is a comprehensive two volume work bringing together both review and original research articles on key topics in nitrogen fixation. Chapters across both volumes emphasize molecular techniques and advanced biochemical analysis approaches applicable to various aspects of biological nitrogen fixation. Volume 1 explores the chemistry and biochemistry of nitrogenases, nif gene regulation, the taxonomy, evolution, and genomics of nitrogen fixing organisms, as well as their physiology and metabolism. Volume 2 covers the symbiotic interaction of nitrogen fixing organisms with their host plants, including nodulation and symbiotic nitrogen fixation, plant and microbial "omics", cyanobacteria, diazotrophs and non-legumes, field studies and inoculum preparation, as well as nitrogen fixation and cereals. Covering the full breadth of current nitrogen fixation research and expanding it towards future advances in the field, Biological Nitrogen Fixation will be a one-stop reference for microbial ecologists and environmental microbiologists as well as plant and agricultural researchers working on crop sustainability.

Leseprobe

Table of Contents

Cover

Title Page

Copyright

Dedication

Preface

References

Acknowledgments

Contributors

Volume 1

Chapter 1: Introduction

1.1 Free-Living Diazotrophs

1.2 Symbiotic Nitrogen-Fixing Bacteria

1.3 Associative Nitrogen-Fixing Bacteria

1.4 Outline of This Book

References

Section 1: Focus Chapters

Chapter 2: Recent Advances in Understanding Nitrogenases and How They Work

2.1 Introduction: Two Types of Nitrogenases Exist

2.2 Occurrence and Relationships among the Group-1 Nitrogenases

2.3 Overview of Properties of Mo-Nitrogenase

2.4 Overview of Properties of V-Nitrogenase and Fe-Nitrogenase

2.5 Structures of the Nitrogenase Component Proteins and their Complexes

2.6 Structures of the MoFe-Protein Prosthetic Groups

2.7 How are Substrates Reduced?

2.8 Where are the Binding Sites for Substrates and Inhibitors?

2.9 How are Electrons and Protons Delivered?

2.10 Some Concluding Remarks

References

Chapter 3: Evolution and Taxonomy of Nitrogen-Fixing Organisms with Emphasis on Rhizobia

3.1 Introduction

3.2 Materials and Methods

3.3 Results

3.4 Discussion

Note

Acknowledgments

References

Chapter 4: Evolution of Rhizobium Nodulation: From Nodule-Specific Genes (Nodulins) to Recruitment of Common Processes

4.1 Nodule Formation in a Nutshell

4.2 Signaling in Symbiosis

4.3 The Indeterminate Nodule

4.4 Signaling Inside the Nodule

4.5

Rhizobium

Symbiosis in

Parasponia

4.6 Actinorhizal N-Fixing Symbiosis

4.7 Arbuscular Mycorrhizal Symbiosis

4.8 Interactions with (Biotrophic) Pathogens

4.9 The Evolution of the

Rhizobium

Nodule Symbiosis

References

Chapter 5: Bioengineering Nitrogen Acquisition in Rice: Promises for Global Food Security

5.1 Introduction

5.2 Primary Nitrogen Uptake and Nitrogen-Use Efficiency: Gene Candidates and Caveats

5.3 The Carbon–Nitrogen Interface and N-Transfer: Removing Enzymatic Bottlenecks

5.4 Nitrogen Fixation: The Holy Grail

5.5 Concluding Remarks

References

Section 2: Chemistry and Biochemistry of Nitrogenases

Chapter 6: An Overview on Fe–S Protein Biogenesis from Prokaryotes to Eukaryotes

6.1 Introduction

6.2 Source of Iron and Sulfur

6.3 Structures and Properties of Fe–S Clusters

6.4 Formation of Fe–S CLUSTERS

6.5 Diverse Functionsof Fe–S Proteins

6.6 Fe–S Cluster Biosynthesis in Prokaryotes

6.7 ISC Assembly Machinery

6.8 The SUF Machinery in Bacteria and Plastids

6.9 F–S Protein Assembly in Eukaryotes

6.10 Mitochondrial Isc Assembly Machinery

6.11 Mitochondrial ISC Export System

6.12 CIA Assembly Apparatus

6.13 Conclusion

Acknowledgments

References

Chapter 7: Biosynthesis of the Iron-Molybdenum Cofactor of Nitrogenase

7.1 Introduction: Dinitrogenase and APO-Dinitrogenase

7.2 NifU and NifS

7.3 NifB: From Simple [Fe–S] Clusters to the Core of FeMo-co

7.4 NifQ: Directing Mo to FeMo-co Synthesis

7.5 NifV and the Incorporation of Homocitrate into FeMo-co

7.6 NifEN: A Node in the FeMo-co Biosynthetic Pathway

7.7 NifH: Nitrogenase Moonlighting Protein

7.8 Metallocluster Carrier (Escort) Proteins

7.9 Conclusion

Acknowledgments

References

Chapter 8: Distribution and Ecological Niches of Nitrogenases

8.1 Introduction

8.2 Alternate Nitrogenases and the Metal Content of the Cofactor

8.3 Distinguishing FeFe-Nitrogenase from VFe-Nitrogenase

8.4 Why Three Nitrogenases?

8.5 Rhodopseudomonas palustris CGA009 and Closely Related Strains

8.6 Control of Expression of Nitrogenase

8.7 Global Diversity of Nitrogen-Fixing Organisms

8.8 Isolation of Diazotrophs Containing Mo-Independent Nitrogenases

8.9 Coincidentally Discovered Novel Genera and Species with Alternate Nitrogenases

8.10 Estimates of Current Global Nitrogen Fixation

8.11 Concluding Remarks

References

Section 3: Expression and Regulation of Nitrogen Fixation Genes and Nitrogenase

Chapter 9: Regulation of nif Gene Expression in Azotobacter vinelandii

9.1 Introduction:

Azotobacter vinelandii

as Paradigm of Nitrogen-Fixing Bacteria

9.2 Methodologies Used to Study Regulation of

nif

Gene Expression in

A. vinelandii

9.3

nif

Genes

9.4 The NifA-NifL-GlnK System: A Dynamic Signal Integrating System that Modulates

nif

Gene Expression

9.5 Perspectives

Acknowledgments

References

Chapter 10: Regulatory Coupling of Nitrogen and Carbon Metabolism in Nitrogen-Fixing Pseudomonas stutzeri A1501

10.1 Introduction

10.2 Global Regulatory Networks Controlling Nitrogen Fixation And Nitrogen Source Utilization in Diazotrophic Proteobacteria

10.3 The Nitrogen Regulatory Cascade in

P. stutzeri

A1501

10.4 Catabolite Repression of Carbon Sources Utilization in

Pseudomonas

10.5 Catabolite Repression Control: Properties of A

crc

Mutant Strain of

P. stutzeri

A1501

10.6 Catabolite Repression Control: Transcriptome Analysis

10.7 Catabolite Repression: The CbrA–CbrB System IN

P. stutzeri

A1501

10.8 CbrAB and NtrBC Overlapping Functions in

P. stutzeri

A1501

10.9 Small Regulatory Noncoding RNAs

10.10 Identification of ncRNA in the Genome of

P. stutzeri

A1501

10.11 Concluding Remarks

Acknowledgments

References

Chapter 11: Regulation of Nitrogen Fixation and Molybdenum Transport in Rhodobacter capsulatus

11.1 Introduction

11.2 Transcriptional Activation of Nitrogen Fixation Genes

11.3 Ammonium Inhibition of Nitrogen Fixation

11.4 Molybdenum Repression of Fe-Nitrogenase and Mo Transport

Acknowledgments

References

Chapter 12: Metabolic Regulation of Nitrogenase Activity in Rhodospirillum rubrum: The Role of PII Proteins and Membrane Sequestration

12.1 Introduction

12.2 The “Switch-Off” Effect at the Molecular Level

12.3 The DraT and DraG Proteins

12.4 Regulation of DraT and DraG Activities

12.5 DraT and DraG in Other Organisms

12.6 Concluding Remarks

Acknowledgment

References

Chapter 13: How Does the DraG–PII Complex Regulate Nitrogenase Activity in Azospirillum brasilense?

13.1 Introduction

13.2 Reversible ADP-Ribosylation Regulates Nitrogenase Activity in

A. brasilense

at a Posttranslational Level

13.3 P

II

Proteins Regulate DraT and DraG Activity

13.4 Conclusions

Acknowledgments

References

Chapter 14: Fe Protein Overexpression Can Enhance the Nitrogenase Activity of Azotobacter vinelandii

14.1 Introduction

14.2 Methods

14.3 Results

14.4 Discussion

14.5 Conclusion

Acknowledgments

References

Chapter 15: FNR-Like Proteins in Rhizobia: Past and Future

15.1 Introduction

15.2 Regulation of the

R. etli fix

Genes: An Overview

15.3 Novel Elements in the Regulatory Cascade of

fix

Genes in

Rhizobium etli

15.4 NnrR Links the Low-Oxygen and N-Oxide Response in

Rhizobium etli

15.5 Conserved Functional Features in FNR-Related Proteins of

R. etli

15.6 Prediction of DNA-Binding Specificity Using Three-Dimensional Models of FNR-Related Proteins of

R. etli

15.7 Prediction of FNR-Related Targets in the Genome of

R. etli

CFN42

15.8 Concluding Remarks

Acknowledgments

References

Section 4: Taxonomy and Evolution of Nitrogen Fixing Organisms

Chapter 16: Exploring Alternative Paths for the Evolution of Biological Nitrogen Fixation

16.1 Introduction

16.2 How Ancient isBiological Nitrogen Fixation?

16.3 What are the Most Deeply Rooted Organisms that Harbor Nitrogenase and Presumably Fix Nitrogen?

16.4 Are Alternative Nitrogenases Evolutionary Ancestors of Mo-Nitrogenase?

16.5 What is the Nature of the Metal Complement of “Uncharacterized Nitrogenases”?

16.6 Is There an Evolutionary Relevance to Nitrogenase Promiscuity?

16.7 What is the Evolutionary Origin of Nitrogenase?

Acknowledgments

References

Chapter 17: Phylogeny, Diversity, Geographical Distribution, and Host Range of Legume-Nodulating Betaproteobacteria: What Is the Role of Plant Taxonomy?

17.1 Introduction

17.2 Burkholderias are Highly Diversified Symbionts of Legumes

17.3 Origin and Diversity of

Cupriavidus

Legume Symbionts

17.4 New Rhizobial Taxa in the Beta and Gamma Subclasses of Proteobacteria?

17.5 Has

Mimosa

Coevolved with Its Symbionts?

17.6 Is There Evidence of Coevolution Between Legumes in the Tribe Mimoseae and Their

Burkholderia

Symbionts?

17.7 Conclusion

Acknowledgments

References

Chapter 18: Bradyrhizobium, the Ancestor of All Rhizobia: Phylogeny of Housekeeping and Nitrogen-Fixation Genes

18.1 Introduction

18.2 State of The Art of The Genus

Bradyrhizobium

18.3 Described Species of

Bradyrhizobium

18.4 Phylogeny Based on The Analysis of Ribosomal Genes

18.5 The Use of The Multilocus Sequence Analysis (MLSA) Approach to Define Taxonomy and Phylogeny of

Bradyrhizobium

18.6 Phylogeny of Nodulation and Nitrogen-Fixation Genes in

Bradyrhizobium

18.7 Concluding Remarks

Acknowledgments

References

Chapter 19: Interaction between Host and Rhizobial Strains: Affinities and Coevolution