Advances in microbial physiology最新文献

Stuart Ferguson made important contributions to our understanding of many aspects of bioenergetics, including the operation of the ATP synthase, all of the steps involved in denitification and the mechanism of cytochrome c biogenesis. In this article, we outline his career and describe the development of his research, highlighting his insights into the role of the bacterial periplasm in electron transport reactions and the diversity of covalent attachment mechanisms of heme to apo-cytochrome c.

Cytochrome bd is a tri-haem copper-free terminal oxidase of many respiratory chains of prokaryotes with unique structural and functional characteristics. As the other membrane-bound terminal oxidases, this enzyme couples the four-electron reduction of oxygen to water with the generation of a proton motive force used for ATP synthesis but the molecular mechanism does not include proton pumping. Beyond its bioenergetic role, cytochrome bd is involved in resistance to several stressors and affords protection against oxidative and nitrosative stress. These features agree with its expression in many bacterial pathogens. The importance for bacterial virulence and the absence of eukaryotic homologues make this enzyme an ideal target for new antimicrobial drugs. This review aims to provide an update on the current knowledge about cytochrome bd in light of recent advances in the structural characterisation of this enzyme, focussing on its reactivity with environmental stressors.

Nitrous oxide is a major contributor towards greenhouse gas emissions from agriculture and is the most significant single cause of ozone depletion in the 21st Century. In this chapter, the microbial processes associated with the production and consumption of nitrous oxide are reviewed, with a focus on the role of NosZ in nitrous oxide removal. Recent developments have led to a recognition that two distinct clades of nosZ exist, and that diversity exists within and between the clades resulting in functional diversity of NosZ in the organisms that carry them. We point out areas where there are knowledge gaps, particularly a lack of exploration of the comparative biochemistry of NosZ from organisms beyond a few laboratory model species. We discuss the importance of considering how nitrous oxide is measured, and the ways in which factors such as evolutionary selection pressure, regulation, and biochemical organisation impact on the eventual activity of nitrous oxide reduction in biological ecological systems. This is followed by a set of perspectives on how we might apply our current and future knowledge to mitigate atmospheric nitrous oxide accumulation for global benefit.

Photosynthesis by (bacterio)chlorophyll-producing organisms ("chlorophototrophy") sustains virtually all life on Earth, providing the biosphere with food and energy. The oxygenic process carried out by plants, algae and cyanobacteria also generates the oxygen we breathe, and ancient cyanobacteria were responsible for oxygenating the atmosphere, creating the conditions that allowed the evolution of complex life. Cyanobacteria were also the endosymbiotic progenitors of chloroplasts, play major roles in biogeochemical cycles and as primary producers in aquatic ecosystems, and act as genetically tractable model organisms for studying oxygenic photosynthesis. In addition to the Cyanobacteriota, eight other bacterial phyla, namely Proteobacteria/Pseudomonadota, Chlorobiota, Chloroflexota, Bacillota, Acidobacteriota, Gemmatimonadota, Vulcanimicrobiota and Myxococcota contain at least one putative chlorophototrophic species, all of which perform a variant of anoxygenic photosynthesis, which does not yield oxygen as a by-product. These chlorophototrophic organisms display incredible diversity in the habitats that they colonise, and in their biochemistry, physiology and metabolism, with variation in the light-harvesting complexes and pigments they produce to utilise solar energy. Whilst some are very well understood, such as the proteobacterial 'purple bacteria', others have only been identified in the last few years and therefore relatively little is known about them - especially those that have not yet been isolated and cultured. In this chapter, we aim to summarise and compare the photosynthetic physiology and central metabolic processes of chlorophototrophic members from the nine phyla in which they are found, giving both a short historical perspective and highlighting gaps in our understanding.

In global biogeochemical networks nitrogen transitions between a number of different oxidation states, from +5 to -3. The two most oxidized states are found in the nitrogen oxyanions nitrate (NO₃^-, +5) and nitrite (NO₂^-, +3). These two oxyanions form an electropositive redox couple, with a midpoint redox potential (pH7) of +430 mV, that enables them to serve as both electron acceptor (nitrate) and electron donor (nitrite) in a range of catabolic and anabolic processes. Several enzymatic systems have been identified that can inter-convert the two oxyanions and couple them to a range of electron transport pathways. Recent literature on nitrate reduction and nitrite oxidation by prokaryotes reveals a great number of meta "omics" studies identifying genes, transcripts or peptides functionally related to the nitrate / nitrite redox couple in a wide range of environments. To fully interpret such data in the context of the environment being studied requires a recognition of the different physiological functions the nitrate / nitrite redox couple is able to support. This, in turn, is related to the biochemical diversity of the enzymes that drive this reversible redox couple in nature. This review seeks to define bioenergetically the different enzymes involved in nitrate-nitrite inter-conversion and relate this to the diverse physiological activities that this redox couple supports.

Dehalococcoides strains grow obligately by respiration with hydrogen as an electron donor and halogenated compounds as terminal electron acceptors, catalysed by a single membrane-integrated protein supercomplex. Many insights have been gained into the respiratory complex based on physiological experiments, biochemical analyses, genome sequencing, and proteomics. Recent data acquired from activity tests with deuterated water and whole cells revealed the mode of energy conservation by this respiratory complex. The data shows that the proton required for periplasmic dehalogenation originates from inside the cell, suggesting an electrogenic protonation of the electron acceptor, while two protons are released into the periplasm by hydrogen oxidation. This surprisingly simple mechanism of pmf generation aligns with the subunit composition of the respiratory complex, the orientation of the subunits in the membrane, the absence of quinones as electron mediators, the rigidity of the cell membrane, as evidenced by its phospholipid fatty acid composition, and with proton channels formed by protonatable amino acid residues identified in the AlphaFold2-predicted structure of one of the membrane-spanning subunits. The respiration model is characterised by: (i) electrogenic protonation of the electron acceptor; (ii) reliance on a single protein complex for pmf generation without quinones; (iii) lack of transmembrane cytochromes; (iv) presence of both redox-active centres on the same side of the membrane, both facing the periplasm; and (v) restriction of the electron flow to periplasmic subunits of the respiratory complex. This type of respiration may represent an ancestral, quinone-free mechanism, offering inspiring new biotechnological applications.

Lactate is a key metabolite that is used as a carbon and energy source. It can also be generated as a metabolic end product, through reduction of pyruvate. Bacterial enzymes involved in lactate generation are classified as NAD⁺-dependent lactate dehydrogenases and are generally involved in production of lactate during fermentation, while NAD⁺-independent lactate dehydrogenases are involved in oxidation of lactate that is linked to reduction of quinone in respiratory or photosynthetic electron transport pathways, or in anaerobic lactate oxidation linked to electron bifurcation during heterotrophic growth. Enzymes specific for D-lactate, L-lactate or both stereoisomers exist and interconversion of D- and L- stereoisomers is catalyzed by a lactate racemase. Expression of operons encoding enzymes and transporters involved in lactate metabolism is regulated in several ways that can include sensing of the presence of L- or D- lactate by transcriptional regulators, control of gene expression through global regulators of carbon metabolism and regulators that respond to iron availability. Sensing of lactate also appears to be an important cue for changes in cell physiology and behavior and in some bacteria it has been shown to influence biofilm formation. Lactate plays a key role in the maintenance of human microbiomes in different niches and dysbiosis is often a result of an imbalance between lactate production and lactate consumption, which is linked to certain pathologies. Lactate is also an important carbon source for some bacterial pathogens and L-lactate has been shown to play a role in the pathogenesis in animal models of infection. Additionally, L-lactate produced by macrophages, neutrophils and epithelial cells may provide an important carbon source of the survival and growth of intracellular pathogens. Understanding of lactate metabolism at the biochemical, cellular and organismal/community level is of major importance in understanding and management of health and disease and in understanding environmental processes.

Disulfide bonds are covalent linkages connecting two cysteine residues. When formed within the same polypeptide, they assist protein folding and enhance protein stability. In principle, disulfide formation could be facilitated by ubiquitous small-molecule oxidants, like oxygen. Instead, it is catalyzed by dedicated oxidative protein folding pathways throughout the tree of life. In bacteria, disulfides are abundant outside the cytoplasm, whereby chemical and mechanical stresses take their toll on protein molecules. The Disulfide Bond Formation (DSB) system in Escherichia coli K-12 has served as the paradigm for bacterial disulfide bond formation and has been, largely, considered a proteome housekeeper. In this article we discuss the central role of the DSB system for protein homeostasis, the unprecedented diversity of DSB proteins across the bacterial phylogeny, and their emerging roles in infectious disease. We also propose that beyond the known uses of DSB components in biotechnology, the DSB system offers promising avenues for the development of next-generation strategies against challenging bacterial pathogens.

Paracoccus denitrificans is a long-established model organism for studies of methylotrophy, the use of one-carbon compounds as sources of energy and carbon. P. denitrificans can use methanol and methylamine as growth substrates, oxidizing both to formaldehyde in the periplasm. Formaldehyde is oxidized to formate and then to carbon dioxide, which is assimilated into biomass via the Calvin cycle. Genes required for the oxidation of methanol, methylamine, formaldehyde and formate are typically expressed only under methylotrophic conditions or during growth on multi-carbon substrates (such as choline) the catabolism of which generates formaldehyde as a product of demethylation reactions. In this article, we review the pathways of methylotrophic metabolism and the proteins involved, before focusing on mechanisms of gene regulation. P. denitrificans has genes encoding calcium- and lanthanide-dependent methanol dehydrogenases. In other methylotrophs, expression of these enzymes is subject to reciprocal regulation according to the presence or absence of lanthanide ions in growth media. This regulatory phenomenon is referred to as the 'lanthanide switch'. We propose a model for the mechanism of the lanthanide switch in P. denitrificans, which extrapolates from relevant information in other methylotrophs and is consistent with prior literature.

We begin by discussing some historical ideas about the natural dynamics of living organisms and their complex states, from the very transient to the very persistent. We classify ultradian rhythms as being more important than most oscillatory behaviour in their distinctive properties. Then we summarise rhythmicity in three yeasts and five representative protist species. Recent discoveries about the single-celled photosynthetic alga Chlamydomonas reinhardii are then discussed as revealed by computer-controlled semi-continuous monitoring: automatic periodic measurement of the rate of phototaxis and chlorophyll a content over extended times for up to 12 days. Methodological approaches for analysing time series are discussed, including the recently developed 'GaMoSEC' procedure, providing published references to the detection and understanding of the complex behaviour of natural systems. Finally, we conclude by summarising the general significance of ultradian rhythms to the vital aspects of the biological timekeeping of coherent functionality of living systems from single-cell organisms to humans from their healthy to declining states.