Biology of the Nitrogen Cycle

Hermann Bothe, Stuart Ferguson, William E. Newton

• Publisher: Elsevier Science
• Year: 2006
• eBook ISBN: 9780080471334
• Topic: Economics
• Subtopic: Economic Theory
• Index: Economics

All organisms require nitrogen to live and grow. The movement of nitrogen between the atmosphere, biosphere, and geosphere in different forms is described by the nitrogen cycle. This book is an activity of the COST 856 Action on Denitrification. It covers all aspects of the N-cycle: chemistry, biology (enzymology, molecular biology), physics, applied aspects (greenhouse effect, N-pollution problems, practices in farming, in waste-water treatment, and more). In this book, leading editors offer the latest research available on dentrification (reduction of nitrates or nitrites commonly by bacteria- as in soil).* Provides details on denitrification and its general role in the environment* Offers latest research in N-Cycle and its reactions* Discusses impacts on various environments: agriculture, wetlands, plants, waste-water treatment and more* The only book available in the field since the last 20 years* Contains 27 chapters written by internationally highly recognized experts in the field* Covers all modern aspects, emphasizes molecular biology and ecology* Written in an easily understandable way

Part I

Denitrification

Outline

Chapter 1: Introduction to the Biochemistry and Molecular Biology of Denitrification

Chapter 2: The Prokaryotic Nitrate Reductases

Chapter 3: Nitrite Reductases in Denitrification

Chapter 4: Nitric Oxide Reductase: Structural Variations and Catalytic Mechanism

Chapter 5: Nitrous Oxide Reductases

Chapter 6: Denitrification in Rhizobia-Legume Symbiosis

Chapter 7: The Dissimilatory Reduction of Nitrate to Ammonia by Anaerobic Bacteria

Chapter 1

Introduction to the Biochemistry and Molecular Biology of Denitrification

Rob J.M. van Spanning,

David J. Richardson,

Stuart J. Ferguson,

Publisher Summary

This chapter provides an overview of the biochemistry and genetics of denitrification in such organisms. It considers the aspects of denitrification that occur in archaea and certain fungi. Denitrification has been mostly studied in Paracoccus denitrificans and Pseudomonas stutzeri and so it describes denitrification for each of these organisms in turn before considering to what extent general principles can be discerned. In recent years, high-resolution crystal structures have become available for these enzymes with the exception of the structure for NO-reductase. In general, the proteins required for denitrification are only produced under (close to) anaerobic conditions, and if anaerobically grown, cells are exposed to O₂ and then the activities of the proteins are inhibited. Specialized denitrifiers, such as P. denitrificans and the denitrifying Pseudomonads, contain more than 40 genes, which encode the proteins that make up a full denitrification pathway. They include the structural genes for the enzymes and e⁻ donors, their regulators as well as many accessory genes required for assembly, cofactor synthesis, and insertion into the enzymes. In contrast, some denitrifiers can only carry out the two central reactions of the pathway and use these activities to support growth, but the cost of maintaining this capability is a very small amount of genome space. It provides insights into the regulation of gene expression and the way in which some denitrification enzymes play different roles in bacteria.

1.1 Introduction

The denitrification part of the N-cycle transforms nitrate (NO₃⁻) into N₂ gas. This is a reductive process and thus is a form of respiration; it occurs in four stages, NO₃⁻ to nitrite (NO₂⁻), NO₂⁻ to nitric oxide (NO), NO to nitrous oxide (N₂O) and N₂O to N₂. All steps within this metabolic pathway are catalysed by complex multisite metalloenzymes with characteristic spectroscopic and structural features [1]. In recent years, high-resolution crystal structures have become available for these enzymes with the exception of the structure for NO-reductase [2]. Further it should be noted that there may be more than one kind of reductase for each step. In general, the proteins required for denitrification are only produced under (close to) anaerobic conditions, and if anaerobically grown cells are exposed to O₂ then the activities of the proteins are inhibited. Thus, for denitrifying organisms, respiration of O₂ usually occurs in preference to the use of N-oxides or oxyanions. The principal aim of this chapter is to give an overview of the biochemistry and genetics of denitrification in such organisms. At the end of each section we shall briefly consider aspects of denitrification that occur in the archaea and certain fungi. Denitrification has been mostly studied in Paracoccus denitrificans and Pseudomonas stutzeri and so we will describe denitrification for each of these organisms in turn before considering to what extent general principles can be discerned.

1.2 Proteins of denitrification

1.2.1 Paracoccus denitrificans

In all bacteria the enzymes of denitrification receive e⁻ from the respiratory chain system that is part of the cytoplasmic membrane. In other words, denitrification is a form of respiration and shares respiratory chain components with the e⁻ transport system that delivers e⁻ to O₂ via terminal oxidases [3, 4]. As far as denitrification-specific components are concerned, we need to start at the ubiquinol/ubiquinone component of the chains. Reduction of ubiquinone to ubiquinol occurs using e⁻ originating from reductants such as NADH, fatty acids, succinate, etc. In denitrification, ubiquinol can be directly oxidized by a membrane-bound respiratory NO₃⁻-reductase (colour Figure A). There is a crystal structure for the corresponding enzyme, usually known as Nar, from Escherichia coli and thus we know in some detail how the enzyme functions. In brief, the ubiquinol is oxidized towards the periplasmic surface of the membrane, with the release of H⁺ to the periplasm but transfer of e⁻ across the membrane to the active site, which is located on a globular domain that protrudes into the cytoplasm. More detail of this enzyme is given in Chapter 2, but the key point to note here is that transfer of e⁻ through Nar, together with H⁺ release and uptake at the two sides of the membrane, generates a H⁺-motive force across the membrane. The location of the site of NO₃⁻ reduction on the cytoplasmic side of the membrane requires a transport system for NO₃⁻ (Figure A, see Color Plate Section). This is believed to be provided by NarK proteins [5]. In P. denitrificans there are two such proteins fused together. Current evidence indicates that one of these proteins catalyses NO₃⁻ symport with one or more H⁺. This would allow entry of NO₃⁻ into the cell to initiate respiration. In the steady state the NO₃⁻ import would be in exchange for NO₂⁻ export to the periplasm, a process that would be e⁻-neutral and thus not affected by, nor dissipating, the H⁺-motive force across the membrane, which, as in all bacteria, has a membrane potential with polarity negative inside the cell.

Figure A Scheme of a full denitrification process in Paracoccus denitrificans. Dashed arrows, N-oxide transport; straight arrows, e-transport. SDH, succinate dehydrogenase; NDH, NADH dehydrogenase; Q, quinone; bc₁, cytochrome bc₁ complex; c₅₅₀, cytochrome c; paz, pseudoazurin; NAR, membrane-bound NO₃⁻-reducta...

Table of contents

• Cover image
• Title page
• Table of Contents
• List of contributors
• Preface
• Part I: Denitrification
• Part II: Biological Nitrogen Fixation
• Part III: Other Reactions of the Nitrogen Cycle
• Part IV: Applications of Reactions of the Nitrogen Cycle, with Emphasis on Denitrification
• Index