"well-written and informative chapters on stress systems ... on high scientific level and with extensive references ... chapters of this book are worth reading" from Erhard Bremer (Marburg, Germany) writing in Biospektrum (2013) 19: 107-111 read more ...

Stress Response in Microbiology Edited by: Jose M. Requena ISBN: 978-1-908230-04-1 Publisher: Caister Academic Press Publication Date: June 2012 Cover: hardback "well-written and informative" (Biospektrum)

"... a comprehensive suite that provides both breadth and depth ... 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. It is has previously been difficult to find research and education resources that provide readable, yet detailed, overviews of N cycle biology and chemistry, and this book nicely couples these high-level overviews that are likely to be highly cited, with a number of very specific topics. I suspect this book will be a major reference for many years to come, despite the rapid pace of research." from Jonathan Zehr (University of California, Santa Cruz, USA) writing in ASM Microbe read more ...

Nitrogen Cycling in Bacteria: Molecular Analysis Edited by: James W. B. Moir ISBN: 978-1-904455-86-8 Publisher: Caister Academic Press Publication Date: July 2011 Cover: hardback "a major reference for many years to come" (ASM Microbe)

"brings together 17 expert groups to review aspects of the stress response in bacteria, mycoplasmas, yeast and a range of protozoans. Chapters are of reasonable size, well (and currently) referenced and show a common style, which is a mark of good editing ... well and sensibly illustrated ... will be of interests to bacteriologists, parasitologists and the growing number of scientists interested in the cell stress response." from Brian Henderson (University College London, UK) writing in Microbiology Today (2012) read more ...

Stress Response in Microbiology Edited by: Jose M. Requena ISBN: 978-1-908230-04-1 Publisher: Caister Academic Press Publication Date: June 2012 Cover: hardback "well and sensibly illustrated" (Micro. Today)

from Julien Brillard and Véronique Broussolle writing in Stress Response in Microbiology:

Among the soil bacteria of the spore former genus Bacillus, the human pathogens mostly belong to the B. cereus group. This species is divided in seven phylogenetic groups, with particular traits in virulence, and particular growth temperature ranges, where each of these seven phylogenetic groups corresponds to a specific "thermotype", showing clear differences in ability to grow at low or high temperatures. After a temperature downshift, changes that occur in the bacterial cell include a decrease of the membrane fluidity, a stabilisation of secondary structures of nucleic acids which consequently causes a decreased efficiency in transcription and translation, a misfolding of some proteins, etc. The bacterial cell response involves various mechanisms which, among the Bacillus genus, have been mostly studied in Bacillus subtilis. This chapter focuses on current research about B. cereus low-temperature adaptation, compared to what is well described in B. subtilis.

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from Isabel Delany and Kate L. Seib writing in Stress Response in Microbiology:

Mechanisms to sense, avoid and scavenge oxidants as well as repair damaged biomolecules are important survival and virulence factors of the obligate human pathogens Neisseria meningitidis and Neisseria gonorrhoeae. These bacteria are routinely exposed to several forms of oxidative and nitrosative stress during colonisation and interaction with the host, of which superoxide, hydrogen peroxide and nitric oxide are some of the key oxidants that result in damage to the bacteria. However, the pathogenic Neisseria express an array of defense mechanisms to combat oxidative and nitrosative stress, such as catalase, superoxide dismutase, nitric oxide reductase, as well as thiol-based defenses and proteins involved in metal homeostasis and repair of damage to DNA and proteins. The expression of these defenses is tightly regulated by a series of transcription factors containing redox-sensitive active sites, including OxyR, Fur, PerR/Zur, FNR, MseR, LexA NsrR, NmlR, which sense and maintain the redox homeostasis of the cell.

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from Alfonso Olivos-García, Emma Saavedra, Erika Rubí Luis-García, Mario Nequiz and Ruy Pérez-Tamayo writing in Stress Response in Microbiology:

Several species belonging to the genus Entamoeba can colonize the mouth or the human gut; only Entamoeba histolytica, however, is pathogenic to the host, causing the disease amebiasis. This illness is responsible for one hundred thousand human deaths per year worldwide, affecting mainly underdeveloped countries. Throughout its entire life cycle, or invasion of human tissues, the parasite is constantly subjected to stress conditions. Under in vitro culture, this microaerophilic parasite can tolerate up to 5% oxygen concentrations; however, during tissue invasion the parasite has to cope with the higher oxygen content found in well perfused tissues (4-14%) and with reactive oxygen and nitrogen species (ROS and NOS, respectively) derived from both host and parasite. In almost all living cells, a low-dose, tightly regulated generation of ROS and NOS mediates several physiological functions such as growth, differentiation and metabolism; an excess of ROS and NOS, however, damages DNA, proteins and lipids, leading to cell death. In this chapter we review the latest findings regarding the physiological and pathological molecular functions of oxidative and nitrosative stresses in E. histolytica and discuss whether the molecules involved in the antioxidant system of the parasite can be appropriate drug targets for the treatment of amebiasis.

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from Ewa WaŁecka and Jacek Bania writing in Stress Response in Microbiology:

L. monocytogenes is a food-borne pathogen widespread in the environment. The majority of human listeriosis is associated with consumption of contaminated food. It has the ability to invade many types of nonphagocytic cells and spread from cell to cell, crossing important barriers in host organism. Despite intensified surveillance in food manufacturing serious cases of listeriosis are still reported. Before L. monocytogenes causes disease it has to endure adverse conditions encountered in food during its processing and storage, such as supraoptimal temperatures, low pH, high osmolarity, presence of oxidants. In the human intestinal tract L. monocytogenes must overcome another set of challenges as the low pH of the stomach, volatile fatty acids, low oxygen levels, osmotic stress, nutrient variability, bile stress and natural flora in the intestine. To survive in hostile environment bacteria adjust their metabolism which involves expression of stress response genes. Consequently, bacteria synthesize proteins that repair damages, maintain the cell stability, eliminate the stress factor, and restore homeostasis. The stress response not only affects L. monocytogenes resistance to subsequent doses of stress factors, but can also alter the pathogen's virulence.

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from Melissa L. Madsen and F. Chris Minion writing in Stress Response in Microbiology:

Because mycoplasmas lack cell walls and have a limited genome capacity, there has been interest in their regulation of gene expression in these unique organisms. Their restriction to the host environment only adds to the intrigue. That environment, however, is not constant, changing with the host adaption to colonization and disease by the mycoplasma. This review focuses on the types of stresses the mycoplasma might encounter in vivo including heat shock, oxidative stress, osmolarity shifts, hormone exposure, and iron deprivation. Biofilm studies are included because of their use by other pathogens as a defense measure to resist killing in the host. The field of mycoplasmology is still in its infancy, particularly in regards to gene regulatory mechanisms. There have even been suggestions that mycoplasmas may not have the capacity to respond to changing environmental conditions. The studies reported here, however, show unequivocally that mycoplasmas do respond to their environment by altering transcription rates. How that is accomplished is still unknown except in one instance, heat shock. In summary, like all bacteria, mycoplasmas respond to their environment. That response may be limited, but it appears essential to their survival.

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from Sylke Müller and Christian Doerig writing in Stress Response in Microbiology:

The life cycle of malaria parasites comprises a complex succession of developmental stages occurring in two different hosts, the human patient and the mosquito vector. In both hosts, the parasite encounters hostile environments and must deal with stresses such as immune responses, sharp temperature shifts and exposure to drugs; partly because of large-scale haemoglobin degradation in the infected erythrocyte and resulting haeme release, oxidative stress is another challenge that the parasite must face. In contrast to other eukaryotes where stress response is largely mediated through a well-defined and robust transcriptional response, it appears that malaria parasites opted for a different strategy. In line with the largely fixed transcriptional programme that characterises the progression of the organisms through their life cycle stages, the transcriptional response to several stresses (such as drug treatments) consists primarily of low-amplitude, genome-wide changes of transcript abundance. However, recent findings suggest that specific transcriptome adaptations, that affect selected aspects of the parasites' physiology, also occur. Overall, the absence in the parasite's kinome of classical stress response mediators such as SAPKs/JNKs, together with the relative scarcity in transcription factors, suggest a low level of flexibility of the parasite in implementing classical eukaryotic stress response pathways. Post-transcriptional mechanisms are expected to play crucial roles in stress response in Plasmodium as exemplified by the demonstrated involvement of an eIF2alpha kinases in response to starvation stress.

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from Marcelo A. Comini, Andrea Medeiros and Bruno Manta writing in Stress Response in Microbiology:

African trypanosomes (Trypanosoma brucei sp.) are unicellular eukaryotic organisms that undergo a complex life cycle shuttling between an invertebrate (vector) and a mammalian host. The parasites have evolved sophisticated and efficient mechanisms to cope with, and adapt to, different environmental conditions. Distinct physical (temperature, pH, osmotic pressure) and biological (endo- and exo-biotic molecules, antibodies, proteases, etc) stimuli acting individually or in a concerted manner induce an adaptive response in the parasite. Depending on the nature and extent of the stress, the cellular response can be transient or long-term and associated with minor or major morphological and metabolic changes. In this chapter we compile the most significant molecular and biological aspects related to the mechanisms and components of the stress response of T. brucei to adapt and survive in the bloodstream of mammals.

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from N. Kaye Horstman and Andrew J. Darwin writing in Stress Response in Microbiology:

Pathogenic Yersinia species have long been studied as important causes of human disease and as model organisms to understand widely conserved mechanisms of bacterial virulence. Like all bacteria, these pathogens must respond to a variety of potentially damaging conditions to ensure their survival. This chapter begins by introducing the pathogenic Yersinia and the aspects of their lifestyles that are likely to require successful response to stress. The emphasis is primarily on conditions relevant to pathogenesis. Then, some genome-wide transcription and gene function studies that have identified or implicated stress response mechanisms are summarized. Next, more focused analyses of response to increased and decreased temperature, encounter with macrophages, and macrophage-like conditions are covered in more detail. Finally, the so-called extracytoplasmic stress responses (ESRs) that are activated by changes to the cell envelope will be described. Several of these ESRs have been directly associated with the infectious process in Yersinia. Inactivation of one, the phage-shock-protein (Psp) system, completely attenuates Y. enterocolitica. As a result, the Psp system has become the most extensively studied Yersinia stress response. Therefore, the final section specifically describes the regulation and function of this critical stress response system.

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from Richard W. Stokes writing in Stress Response in Microbiology:

There are many species of mycobacteria, some of which are pathogens of man. Mycobacterium tuberculosis, the etiological agent of tuberculosis, is a major pathogen of man with about one third of the world's population being infected. It resides within host macrophages where it can survive in a dormant state for the lifetime of the host with about 10% of all infections resulting in disease. This environment results in the bacteria being exposed to numerous stresses including nutrient deprivation, reduced oxygen availability, exposure to pH changes and exposure to the antimicrobial activities of the host's cell-mediated immune response. The bacterium responds with its own defense mechanisms that include the increased expression of stress proteins (also called heat shock proteins). This review describes the regulation and function of the major stress proteins within mycobacteria such as the GroEL, GroES and DnaK homologues along with hspX (alpha-crystallin) and others. The multiple copies of cpn60 (GroEL homologue) that are found within mycobacteria are discussed along with their putative roles as chaperonins but also as "moonlighting" proteins with roles in immunomodulation and receptor/ligand interactions that facilitate the pathogenesis of M. tuberculosis.

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from Suzanne Humphrey, Tom J. Humphrey and Mark A. Jepson writing in Stress Response in Microbiology:

Salmonella enterica are the causative agents of a spectrum of diseases, including enteric fever and self-limiting gastroenteritis and remain significant foodborne pathogens throughout both the developed and developing worlds. The ability to actively invade and reside within gut epithelia and macrophages is an important process in the establishment of Salmonella infection, generating localised inflammatory responses and facilitating systemic spread of the pathogen within the host. Many environments, including food matrices, the external environment and conditions within the host, present a range of stressful challenges that Salmonella must overcome in order to survive and establish infection. Salmonella utilise a diverse range of stress response strategies, including expression of alternative RNA polymerase sigma factors, uptake of compatible solutes, increased expression of genes encoding uptake or efflux pumps, and production of proteins with roles in protecting and repairing stress-induced damage, in order to facilitate their survival in suboptimal and stressful growth environments. Additionally, the ability of Salmonella to undergo morphological changes during stress exposure and rapidly recover from stress conditions commonly encountered within food matrices represents a pertinent issue for food processing and public health.

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from Jacqueline Abranches and Josá A. Lemos writing in Stress Response in Microbiology:

The genus Streptococcus is comprised of a diverse group of organisms, which includes food-associated, commensal and pathogenic species. The importance of this genus to the food industry and the capacity of certain species to infect animals and humans make streptococci one of the best-studied Gram-positive bacteria. In this chapter, we will describe the stress responses of the four major pathogenic streptococcal species: Streptococcus mutans, the etiologic agent of dental caries, S. pyogenes (commonly known as Group A Streptococcus or GAS), responsible for a variety of suppurative disesases as well as life-threatening invasive infections and post-infection sequelae, S. agalactiae (Group B Streptococcus or GBS), a major bacterial pathogen associated with neonatal infections, and S. pneumoniae, the leading causative agent of bacterial pneumoniae. In the following pages, the description of the stress response mechanisms for each individual species is presented in the context of the environmental stress condition. In addition to highlighting the cross-species conservation of certain stress reponses, this organization will allow the reader to follow the progresses obtained in each species, and, at the same time, identify areas that have been poorly explored.

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from Eulàlia de Nadal and Francesc Posas writing in Stress Response in Microbiology:

Adaptation to environmental stress requires changes in many aspects of cellular physiology essential for cell survival, such as gene expression, translation, metabolism, morphogenesis or cell cycle progression. Accordingly, the ability of eukaryotic cells to survive and thrive within adverse environments depends on rapid and robust stress responses. Stress-activated protein kinases (SAPKs) pathways are key elements on intracellular stress-signalling networks to respond and adapt to extracellular changes. In this review, we describe the different mechanisms used by model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, as well as the pathogenic fungus Candida albicans, to sense and transduce stress signals to SAPKs in response to osmo, heat and oxidative stresses. Moreover, other signalling pathways related to stress are discussed. Although much remains to be learned, studies from yeast have served to understand how stress signalling molecules adjust precise and efficient adaptation strategies to maximize cell survival in response to extracellular stimuli.

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from Turán P. Ürményi, Deivid C. Rodrigues, Rosane Silva and Edson Rondinelli writing in Stress Response in Microbiology:

Trypanosoma cruzi, the causal agent of Chagas' disease, is a flagellated protozoan parasite with a complex life cycle that involves infecting an insect and a mammalian host. Several environmental stresses occur during its life cycle, such as heat, reactive oxygen species, and osmolarity changes, and the parasite has evolved a variety of stress responses to cope with these challenges. The stress responses range from synthesis of several proteins and small molecules to modulation of the activity of organelles, and they are essential for the parasite's viability and survival in both hosts. Here we review the components and operation of T. cruzi's stress response with emphasis on its relevance to the parasite's biology and to Chagas' disease transmission, pathogenesis and treatment.

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from Jose M. Requena writing in Stress Response in Microbiology:

Leishmania parasites are unicellular protozoa descending from one of the oldest eukaryotic lineages. During its digenetic life cycle, Leishmania alternates between the alimentary tract of the sandfly vector as an extracellular promastigote and the acidic phagolysosomes of macrophage cells as an intracellular amastigote. Parasites must cope with varied and heterogeneous environments: changes in temperature, in pH, in nutrient and oxygen concentrations. Also, they must face the immune defences, such as complement factors, free radicals and other antimicrobial effectors. The focus of this chapter will be on our current knowledge of the different stress responses in Leishmania, ranging from description of the prototypical heat shock response to more specific responses found in this parasite. A comprehensive view on the implications of the stress response in parasite survival, in cytodifferentiation and in apoptotic processes will be presented. Future studies, which should be directed mainly to the uncovering of the stress sensors, signal transduction pathways and regulatory mechanisms leading to the induction of the appropriate stress response will be also discussed.

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from Juan A. Ayala, Felipe Cava and Miguel A. de Pedro writing in Stress Response in Microbiology:

The cell envelope is the major line of defence against environmental threats. It is an essential but vulnerable structure that shapes the cell and counteracts the turgor pressure. It provides a sensory interface, a molecular sieve and a structural support, mediating information flow, transport and assembly of supramolecular structures. Therefore, maintenance of cell envelope integrity in the presence of deleterious conditions is crucial for survival. Several envelope stress responses, including two components regulatory systems (TCRS), of Escherichia coli are involved in the maintenance, adaptation and protection of the bacterial cell wall in response to a variety of stresses. Recent studies indicate that these stress responses exist in many Gram negative pathogens. Particular emphasis has been made on the identified TCRS and their activating signals. Another aspect of stress response is the generation of morphological modifications. Most bacteria alter shape when growth conditions change and upon symbiotic or parasitic processes. Any modification in cell shape is connected with cell wall metabolism and requires specific regulatory mechanisms. Recent advances support the existence of complex mechanisms mediating morphological responses to stress involving inter and intra-specific signalling.

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from W. Brian Whitaker and E. Fidelma Boyd writing in Stress Response in Microbiology:

Members of the genus Vibrio are Gram-negative ubiquitous marine bacteria. They can be isolated directly from the water column but are perhaps most known for their association with eukaryotic organisms. In their association with eukaryotic hosts, be it pathogenic or symbiotic, these bacteria must respond to a variety of stress conditions present within the host environment. Often times, these stress response systems are vitally important for the vibrios to successfully establish in the host. Here, we will discuss the systems used by the three main human pathogens of the genus, V. cholerae, V. parahaemolyticus, and V. vulnificus as well as briefly discussing the stress response systems of V. fischeri, V. splendidus, and V. anguillarum, all of which form close associations with marine organisms.

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from Maria J. Figueras, Sergio O. Angel, Verónica M. Cóceres and Maria L. Alomar writing in Stress Response in Microbiology:

Toxoplasma gondii is an important pathogen of human and domestic animals. It has a complex life cycle which includes the transition from one host to another, being only exposed to the environment during one stage, as highly resistant oocysts. Interestingly, in the intermediate host (non-feline mammalians and birds) the parasite presents an asexual cycle with two stages that can interconvert without its passage in the definite host (felines). The asexual cycle is very important in the establishment of the infection and on its pathogenesis and it could be driven by different kind of stressors. Therefore, the response to environmental and host stresses is essential to their viability and successful progression through their life cycle. The heat shock proteins are key molecules not only in the resistance to different stressors, but they are also involved in the optimal differentiation as well as in other biological processes in T. gondii. This chapter summarizes the findings on different aspects of T. gondii stress responses and the implication of these processes in the biology and pathogenesis of this parasite.

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from Stephen Spiro writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

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from Elizabeth M. Baggs and Laurent Philippot writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

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from Cristina Sánchez, Eulogio J. Bedmar and María J. Delgado writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

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from John W. Peters, Eric S. Boyd, Trinity Hamilton and Luis M. Rubio writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

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from Marc Strous writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

Further reading: Nitrogen Cycling in Bacteria: Molecular Analysis

from James W. B. Moir writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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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from Shilpa Bali and Stuart J. Ferguson writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

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from Jörg Simon writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

Further reading: Nitrogen Cycling in Bacteria: Molecular Analysis

from Rob J.M. van Spanning writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

Further reading: Nitrogen Cycling in Bacteria: Molecular Analysis

from Robert van Lis, Anne-Lise Ducluzeau, Wolfgang Nitschke and Barbara Schoepp-Cothenet writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

Further reading: Nitrogen Cycling in Bacteria: Molecular Analysis

from David Richardson writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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.

Further reading: Nitrogen Cycling in Bacteria: Molecular Analysis

from Conrado Moreno-Vivián, Víctor M. Luque-Almagro, Purificación Cabello, M. Dolores Roldán and Francisco Castillo writing in Nitrogen Cycling in Bacteria: Molecular Analysis:

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).

Further reading: Nitrogen Cycling in Bacteria: Molecular Analysis