Nitrogen Cycling in Bacteria: Molecular Analysis
"a snapshot of the current understanding" (Book News)
"strongly recommended" (Microbiol. Today)
"a major reference for many years to come" (ASM Microbe)
Caister Academic Press
James W. B. Moir
Department of Biology, University of York, Heslington, York YO10 5YW, UK
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Microorganisms that convert gaseous nitrogen (N2) to a form suitable for use by living organisms are pivotal for life on earth. Another set of microbial reactions utilise the bioavailable nitrogen creating N2 and completing the cycle. This crucial nutrient cycle has long been the subject of extensive research, and recently advances in studying the biochemistry, bioinformatics, cell biology, and the physiology of bacterial nitrogen cycling processes, alongside the advent of the omics age, have had a massive impact, amongst other things, enabling us to fully appreciate the sheer diversity of approaches adapted by individual organisms. Research in this area is at a very exciting stage.
This timely book aims to provide comprehensive reviews of current nitrogen cycle research and to give a broader perspective on the state of our understanding of this key biogeochemical cycle. With contributions from expert authors from around the world, topics covered include: the archaean N-cycle; redox complexes N-cycle; organisation of respiratory chains in N-cycle processes; Mo-nitrogenase; nitrogen assimilation in bacteria; alternative routes to dinitrogen; nitrite and nitrous oxide reductases; assembly of respiratory proteins; nitric oxide metabolism; denitrification in legume-associated endosymbiotic bacteria; nitrous oxide production in the terrestrial environment; bacterial nitrogen cycling in humans. This book will serve as a valuable reference work for everyone working in this field and will also be of interest to researchers studying symbioses, environmental microbiology, plant metabolism, infection events and other prokaryote-eukaryote interactions.
"a snapshot of the current understanding of the nitrogen cycle in bacteria" from Ref. Res. Book News (August 2011)
"The scope of the book is nicely balanced ... very refreshingly, describes aspects relevant to all of the classical stages of the N cycle in several individual chapters ... (the book) is relevant to all of us studying some aspect of the N cycle and is strongly recommended as a core reference that should be owned by every research group working in this area." from Microbiol. Today (2011)
"... provides a rich resource for the researcher, student, and educator ... an important reference book that provides a current overview of the biochemical underpinnings of the major features of the N cycle, while also providing some topical examples of the details of the N cycle in several environments, including plant symbiosis, the terrestrial environment, and the human microbiome ... likely to be highly cited ... this book will be a major reference for many years to come" from ASM Microbe
Table of contents
1. The Nitrogen Cycle in the Archaean: An Intricate Interplay of Enzymatic and Abiotic Reactions
Robert van Lis, Anne-Lise Ducluzeau, Wolfgang Nitschke and Barbara Schoepp-Cothenet
On modern planet Earth, a multitude of nitrogen cycle enzymes equilibrate the atmospheric reservoir of dinitrogen with the more oxidized and more reduced nitrogen compounds essential for life. The respective enzymes are elaborate entities and the reactions performed are complicated and in cases energetically challenging. Nitrogen, however, must have been a crucial element already at life's very beginnings which raises the question how the primordial nitrogen cycle of emerging life in the Archaean - necessarily using simpler and likely fewer enzymes - may have evolved into the very complex network of present planet Earth. To address this question, we have analysed molecular phylogenies of the presently known enzymes involved in the present day nitrogen cycle. The results collected and presented in this chapter indicate that in the Archaean, the enzymatic part of this cycle was restricted to a partial segment of the modern energy conserving denitrification pathway and that abiotic redox conversions of nitrogen specific to the geoenvironment of the Archaean were the evolutionary precursors of many reactions now requiring enzyme catalysis. As found in recent years for other core metabolic processes, the biological nitrogen cycle appears to be evolutionarily rooted in inorganic chemistry.
2. The Redox Complexes of the Nitrogen Cycle
The redox reactions of the nitrogen cycle comprise a large number of oxidative and reductive reactions that are catalysed by wide variety of enzymes with different catalytic centres. These enzymes are frequently organised as multi-protein complexes and in some recently emerging cases enzymes catalysing different reactions of the N-cycle appear to form super-complexes. This review will survey some of these N-cycle protein complexes.
3. Organisation of Respiratory Electron Transport Chains in Nitrate-Reducing and Nitrifying Bacteria
Nitrogen compounds serve as electron donor and electron acceptor substrates in several modes of microbial respiration such as nitrification, nitrate reduction, denitrification and nitrite ammonification. There are several well-established model bacteria for each of these processes and in many, though not all, cases the various dehydrogenases and reductases involved in the conversion of nitrogen compounds have been thoroughly characterized including the determination of high-resolution structure models. On the other hand, the architecture of complete respiratory electron transport chains is often less-well known, especially with respect to donor:quinone dehydrogenase and quinol:acceptor reductase systems that connect the membranous quinone/quinol pool to the oxidative or reductive part of an electron transport chain. Notably, a rather limited number of redox-active protein modules has evolved that is employed by different bacteria in a versatile manner. Occasionally, bacterial species even display different electron transport chain set-ups despite using the same type of substrate-converting enzyme. This article highlights commonalities and differences in the organisation of bacterial respiratory electron transport chains that are involved in environmentally important N-cycle processes and discusses the relevance of this knowledge in the context of microbial bioenergetics and (meta)genomics.
4. Biochemistry of Mo-Nitrogenase
John W. Peters, Eric S. Boyd, Trinity Hamilton and Luis M. Rubio
The large majority of biological nitrogen fixation occurs by the activity of Mo-nitrogenase. Mo-nitrogenase is found in a wide variety of bacteria and some Archaea and is a complex two component enzyme that contains multiple metal-containing prosthetic groups. The biochemistry of nitrogenase has a rich history and the enzyme is a model system for examining more general processes in biology such as electron transfer, metal-cofactor assembly, and even nucleotide dependent signal transduction. In addition, studies examining nitrogenase has pushed the envelope in terms of the practical application of various spectroscopic methods. This chapter treats the historical perspective and development of key advances in our understanding of the biochemistry of Mo-nitrogenase from its infancy and early beginnings in the 1960s to the state of the field today.
5. Transport and Assimilation of Inorganic Nitrogen in Bacteria
Conrado Moreno-Vivián, Víctor M. Luque-Almagro, Purificación Cabello, M. Dolores Roldán and Francisco Castillo
The incorporation of inorganic nitrogen into cell material is known as nitrogen assimilation. Usually, ammonium is the preferred inorganic nitrogen source for microorganisms. Ammonium assimilation requires the transport of this ion into the cells and its further incorporation into carbon skeletons, mainly through the glutamine synthetase-glutamate synthase pathway. Alternatively, glutamate dehydrogenase may also contribute to ammonium assimilation under certain conditions. Glutamine synthetase is the key enzyme for the regulation of ammonium assimilation; its activity is usually controlled by reversible covalent modification or feedback mechanisms and, at the gene expression level, transcription is often controlled by general nitrogen regulatory systems that vary depending on the organisms. In addition, ammonium transport is also subjected to regulation by carbon and nitrogen availability. Oxidized nitrogen compounds like nitrate and nitrite may be also used as nitrogen sources by many bacteria and archaea. Nitrate assimilation requires nitrate transport into the cells and two enzymes, nitrate and nitrite reductases, which catalyze the two-electron reduction of nitrate to nitrite and the six-electron reduction of nitrite to ammonium, respectively. These assimilatory enzymes are structural and functionally different to respiratory nitrate and nitrite reductases. Control of nitrate assimilation in different organisms may involve distinct regulatory proteins and mechanisms, but usually the process is regulated by nitrate and/or nitrite induction (pathway-specific control) and by ammonium repression (general nitrogen control).
6. Beyond Denitrification: Alternative Routes to Dinitrogen
Although nitrate is a powerful electron acceptor, it was generally believed that it could not be used to activate recalcitrant substrates such as ammonium and methane. Only in the past decades, bacteria were identified that could activate these compounds. These bacteria have become known as anaerobic ammonium oxidizing ('anammox') bacteria and 'denitrifying methanotrophs'. Each makes use of a different and so far unique pathway of nitrate reduction with dinitrogen gas as the end product. Anammox bacteria activate ammonia with nitric oxide, leading to the production of hydrazine (N2H4). Denitrifying methanotrophs dismutate two molecules of nitric oxide into molecular oxygen (O2) and nitrogen (N2). In this chapter bacteria, pathways, cell biology and environmental relevance are discussed.
7. Structure, Function, Regulation and Evolution of the Nitrite and Nitrous Oxide Reductases: Denitrification Enzymes With a Beta-Propeller Fold
Rob J.M. van Spanning
Specialized denitrifiers recruit 2 β-propeller enzymes in their anaerobic nitrate respiratory electron transfer network, one of which is an iron containing cd1-type nitrite reductase, termed NirS, and the other is a copper containing nitrous oxide reductase, NosZ. Together they complement a full denitrification pathway along with nitrate and nitric oxide reductases for the sequential reduction of nitrate to dinitrogen gas. These enzymes are tightly controlled on the level of expression and activity not only according to an energetic hierarchy but also to ensure a balanced conversion of the N-oxides and to prevent the accumulation of the toxic intermediates nitrite and nitric oxide. The adaptive response during the switch from aerobic respiration to denitrification is orchestrated by a dedicated signal transduction network that integrates environmental and intracellular signals and passes these on to the DNA. Amongst these signals are oxygen, denitrification intermediates (nitrate, nitrite, nitric oxide), the redox state of the respiratory components, and metal availability (copper, iron). The coordinate acquisition of these metals during the oxic-anoxic shift is a challenge since their bioavailability requires different reduction states and oxygen tensions.
8. Assembly of Respiratory Proteins of the Nitrogen Cycle
Shilpa Bali and Stuart J. Ferguson
The respiratory reactions of the nitrogen cycle are those of denitrification, the successive reductions of nitrate, nitrite, nitric oxide and nitrous oxide to nitrogen gas, and those of nitrification, oxidation of ammonium first to nitrite and then to nitrate. These reactions are catalysed by enzymes containing one or more of the cofactors, heme (non-covalent as in b-type hemes, or covalent as in c-type hemes), iron sulphur, molybdenum and copper centres. With the exception of molybdenum, these redox active cofactors are also integral to the operation of the respiratory chain systems that deliver electrons to and from the individual enzymes. This chapter gives an overview of current knowledge about how each of these cofactor types is attached to their respective apo-proteins, in the context that many of the proteins are located on the periplasmic side of the membrane and delivery to that compartment is either as an unfolded protein, and thus mediated by the sec system, or as a folded protein and thus facilitated by the tat system.
9. Nitric Oxide Metabolism: Physiology and Regulatory Mechanisms
Nitric oxide (NO) is synthesised in bacteria as a product of the reduction of nitrite or the oxidation of arginine. NO is growth inhibitory, due to its ability to inhibit respiratory oxidases and [Fe-S] cluster containing dehydratases. NO also reacts with oxygen and biologically relevant oxygen radicals (such as superoxide) to generate a number of other toxic reactive nitrogen species. NO detoxification is typically accomplished by oxidation to nitrate, or reduction to nitrous oxide or ammonia, and these activities have been associated with a variety of enzymes. In many cases, expression of the genes encoding NO detoxification activities is controlled by NO-sensitive regulatory proteins. This Chapter describes the different pathways for NO synthesis and consumption in bacteria, and the mechanisms and roles of the associated regulatory proteins. The Chapter also reviews the growing body of evidence that implicates NO in regulating other physiological processes, including [Fe-S] cluster biogenesis, metabolism, motility and biofilm development.
10. Denitrification in Legume-associated Endosymbiotic Bacteria
Cristina Sánchez, Eulogio J. Bedmar and María J. Delgado
Rhizobia are soil, Gram-negative bacteria with the unique ability to establish a N2-fixing symbiosis on legume roots and on the stems of some aquatic legumes. During this interaction bacteroids, as rhizobia are called in the symbiotic state, are contained in intracellular compartments within a specialized organ, the nodule, where they fix N2. When faced with a shortage of oxygen some rhizobia species are able to switch from O2-respiration to using nitrates to support respiration in a process known as denitrification. The complete denitrification pathway comprises the sequential reduction of nitrate or nitrite to dinitrogen, via the gaseous intermediates nitric oxide and nitrous oxide. The enzymes involved in denitrification are nitrate-, nitrite-, nitric oxide- and nitrous oxide reductase, encoded by nar/nap, nir, nor and nos genes, respectively. In recent years it has emerged that many rhizobia species have genes for enzymes of some or all of the four reductase reactions for denitrification. In fact, denitrification can be readily observed in many rhizobia species, in their free-living form, in legume root nodules, or in isolated bacteroids. This chapter will focus on update progress on denitrification by rhizobia under free-living and symbiotic conditions.
11. Nitrous Oxide Production in the Terrestrial Environment
Elizabeth M. Baggs and Laurent Philippot
Terrestrial ecosystems are a major source of nitrous oxide (N2O), with soils accounting for ~70% of the atmospheric loading of this greenhouse gas. Here we provide a synthesis of current understanding of the environmental regulation of N2O production and reduction through different microbial pathways, presenting examples of where measured emissions have been related to characterizations of the underpinning microbial communities. We explore the direct and indirect influence of plants on rhizosphere N2O production, reduction and net emission, and the interactions between N2O production and methane oxidation, as examples of coupling between the C and N cycles that need to be considered when developing appropriate and more targeted strategies for greenhouse gas mitigation.
12. Bacterial Nitrogen Cycling in the Human Body
James W. B. Moir
Surfaces of the human body exposed to the environment are heavily colonised by bacteria. The bacteria that live in these environments are frequently exposed to anoxia and to nitric oxide which is generated by the host. Dealing with these two environmental factors often involves implementing nitrogen cycle processes to (i) maintain growth and survival by respiration in the absence of oxygen, and (ii) detoxify the free radical nitric oxide. In this chapter I explore the nitrogen cycling processes relevant to the human body environment. Whilst microbial colonisation is part of the normal physiology of the human body, the body can also be exposed to pathogenic bacteria which also utilise nitrogen cycling processes. Specific sections deal with the processes and consequences of nitrogen cycling by key human pathogens Pseudomonas aeruginosa, Mycobacterium tuberculosis and the pathogenic Neisseria species N. meningitidis and N. gonorrhoeae.
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(EAN: 9781904455868 9781912530632 Subjects: [microbiology] [bacteriology] [molecular microbiology] [environmental microbiology] )