-
Role of the ubiquinone-synthesizing UbiUVT pathway in adaptation to changing respiratory conditions.MBio Aug 2023Isoprenoid quinones are essential for cellular physiology. They act as electron and proton shuttles in respiratory chains and various biological processes. and many...
Isoprenoid quinones are essential for cellular physiology. They act as electron and proton shuttles in respiratory chains and various biological processes. and many α-, β-, and γ-proteobacteria possess two types of isoprenoid quinones: ubiquinone (UQ) is mainly used under aerobiosis, while demethylmenaquinones (DMK) are mostly used under anaerobiosis. Yet, we recently established the existence of an anaerobic O-independent UQ biosynthesis pathway controlled by , , and genes. Here, we characterize the regulation of genes in . We show that the three genes are transcribed as two divergent operons that are both under the control of the O-sensing Fnr transcriptional regulator. Phenotypic analyses using a mutant devoid of DMK revealed that UbiUV-dependent UQ synthesis is essential for nitrate respiration and uracil biosynthesis under anaerobiosis, while it contributes, though modestly, to bacterial multiplication in the mouse gut. Moreover, we showed by genetic study and O labeling that UbiUV contributes to the hydroxylation of ubiquinone precursors through a unique O-independent process. Last, we report the crucial role of in allowing to shift efficiently from anaerobic to aerobic conditions. Overall, this study uncovers a new facet of the strategy used by to adjust its metabolism on changing O levels and respiratory conditions. This work links respiratory mechanisms to phenotypic adaptation, a major driver in the capacity of to multiply in gut microbiota and of facultative anaerobic pathogens to multiply in their host. IMPORTANCE Enterobacteria multiplication in the gastrointestinal tract is linked to microaerobic respiration and associated with various inflammatory bowel diseases. Our study focuses on the biosynthesis of ubiquinone, a key player in respiratory chains, under anaerobiosis. The importance of this study stems from the fact that UQ usage was for long considered to be restricted to aerobic conditions. Here we investigated the molecular mechanism allowing UQ synthesis in the absence of O and searched for the anaerobic processes that UQ is fueling in such conditions. We found that UQ biosynthesis involves anaerobic hydroxylases, that is, enzymes able to insert an O atom in the absence of O. We also found that anaerobically synthesized UQ can be used for respiration on nitrate and the synthesis of pyrimidine. Our findings are likely to be applicable to most facultative anaerobes, which count many pathogens (, , and ) and will help in unraveling microbiota dynamics.
Topics: Animals; Mice; Escherichia coli; Ubiquinone; Nitrates; Quinones; Terpenes
PubMed: 37283518
DOI: 10.1128/mbio.03298-22 -
Microbial Genomics Nov 2023Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles...
Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in , probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of , and sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.
Topics: Anaerobiosis; Mitochondria; Eukaryota; Iron; Sulfates
PubMed: 37994879
DOI: 10.1099/mgen.0.001143 -
The ISME Journal Nov 2023A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be...
A major challenge in managing and engineering microbial communities is determining whether and how microbial community responses to environmental alterations can be predicted and explained, especially in microorganism-driven systems. We addressed this challenge by monitoring microbial community responses to the periodic addition of the same feedstock throughout anaerobic digestion, a typical microorganism-driven system where microorganisms degrade and transform the feedstock. The immediate and delayed response consortia were assemblages of microorganisms whose abundances significantly increased on the first or third day after feedstock addition. The immediate response consortia were more predictable than the delayed response consortia and showed a reproducible and predictable order-level composition across multiple feedstock additions. These results stood in both present (16 S rRNA gene) and potentially active (16 S rRNA) microbial communities and in different feedstocks with different biodegradability and were validated by simulation modeling. Despite substantial species variability, the immediate response consortia aligned well with the reproducible CH production, which was attributed to the conservation of expressed functions by the response consortia throughout anaerobic digestion, based on metatranscriptomic data analyses. The high species variability might be attributed to intraspecific competition and contribute to biodiversity maintenance and functional redundancy. Our results demonstrate reproducible and predictable microbial community responses and their importance in stabilizing system functions.
Topics: Anaerobiosis; Microbiota; Biodiversity; RNA, Ribosomal, 16S; RNA, Ribosomal; Bioreactors; Microbial Consortia
PubMed: 37666974
DOI: 10.1038/s41396-023-01505-x -
Microbiology Spectrum Dec 2023Aromatic compounds are globally abundant organic molecules with a multitude of natural and anthropogenic sources, underpinning the relevance of their biodegradation....
Aromatic compounds are globally abundant organic molecules with a multitude of natural and anthropogenic sources, underpinning the relevance of their biodegradation. EbN1 is a well-studied environmental betaproteobacterium specialized on the anaerobic degradation of aromatic compounds. The here studied responsiveness toward phenol in conjunction with the apparent high ligand selectivity (non-promiscuity) of its PheR sensor and those of the related -cresol (PcrS) and -ethylphenol (EtpR) sensors are in accord with the substrate-specificity and biochemical distinctiveness of the associated degradation pathways. Furthermore, the present findings advance our general understanding of the substrate-specific regulation of the strain's remarkable degradation network and of the concentration thresholds below which phenolic compounds become essentially undetectable and as a consequence should escape substantial biodegradation. Furthermore, the findings may inspire biomimetic sensor designs for detecting and quantifying phenolic contaminants in wastewater or environments.
Topics: Phenol; Phenols; Rhodocyclaceae; Biodegradation, Environmental; Anaerobiosis
PubMed: 37823660
DOI: 10.1128/spectrum.02100-23 -
ELife Apr 2024Metabolic pathways are plastic and rapidly change in response to stress or perturbation. Current metabolic profiling techniques require lysis of many cells, complicating...
Metabolic pathways are plastic and rapidly change in response to stress or perturbation. Current metabolic profiling techniques require lysis of many cells, complicating the tracking of metabolic changes over time after stress in rare cells such as hematopoietic stem cells (HSCs). Here, we aimed to identify the key metabolic enzymes that define differences in glycolytic metabolism between steady-state and stress conditions in murine HSCs and elucidate their regulatory mechanisms. Through quantitative C metabolic flux analysis of glucose metabolism using high-sensitivity glucose tracing and mathematical modeling, we found that HSCs activate the glycolytic rate-limiting enzyme phosphofructokinase (PFK) during proliferation and oxidative phosphorylation (OXPHOS) inhibition. Real-time measurement of ATP levels in single HSCs demonstrated that proliferative stress or OXPHOS inhibition led to accelerated glycolysis via increased activity of PFKFB3, the enzyme regulating an allosteric PFK activator, within seconds to meet ATP requirements. Furthermore, varying stresses differentially activated PFKFB3 via PRMT1-dependent methylation during proliferative stress and via AMPK-dependent phosphorylation during OXPHOS inhibition. Overexpression of induced HSC proliferation and promoted differentiated cell production, whereas inhibition or loss of suppressed them. This study reveals the flexible and multilayered regulation of HSC glycolytic metabolism to sustain hematopoiesis under stress and provides techniques to better understand the physiological metabolism of rare hematopoietic cells.
Topics: Animals; Mice; Adenosine Triphosphate; Anaerobiosis; Glycolysis; Hematopoiesis; Hematopoietic Stem Cells; Oxidative Phosphorylation; Phosphofructokinase-2; Phosphoric Monoester Hydrolases
PubMed: 38573813
DOI: 10.7554/eLife.87674 -
Journal of Environmental Management Jan 2024Anaerobic Digestion (AD) technology emerges as a viable solution for managing municipal organic waste, offering pollution reduction and the generation of biogas and... (Review)
Review
Anaerobic Digestion (AD) technology emerges as a viable solution for managing municipal organic waste, offering pollution reduction and the generation of biogas and fertilisers. This study reviews the research works for the advancements in AD implementation to effectively impact the UN Sustainable Development Goals (SDGs). Furthermore, the study critically analyses responsible waste management that contributes to health and safety, elevating quality of life in both rural and urban areas and, finally, creates a map of AD outputs onto all 17 SDGs. Finally, the assessment employs the three sustainability pillars (i.e., economic, environmental, and social perspectives) to examine the direct and indirect links between AD and all 17 UN SDGs. The findings reveal substantial progress, such as poverty reduction through job creation, bolstering economic growth (SDGs 1, 8, 10, 12), enhancing agricultural productivity (SDG 2), advancing renewable energy usage and diminishing reliance on fossil fuels (SDG 7), fostering inclusive education and gender equality (SDGs 4, 5, 9), combating climate change (SDG 13), transforming cities into sustainable and harmonious environments (SDGs 11, 16, 17), and curbing environmental pollution (SDGs 3, 6, 12, 14, 15). Nonetheless, the study highlights the need for further efforts to achieve the SDG targets, particularly in part of liquid and solid fertilisers as the AD outputs.
Topics: Sustainable Development; Quality of Life; Anaerobiosis; Fertilizers; Cities; Goals
PubMed: 37918233
DOI: 10.1016/j.jenvman.2023.119458 -
Frontiers in Immunology 2023The environmental bacterium causes the often fatal and massively underreported infectious disease melioidosis. Antigens inducing protective immunity in experimental...
INTRODUCTION
The environmental bacterium causes the often fatal and massively underreported infectious disease melioidosis. Antigens inducing protective immunity in experimental models have recently been identified and serodiagnostic tools have been improved. However, further elucidation of the antigenic repertoire of during human infection for diagnostic and vaccine purposes is required. The adaptation of to very different habitats is reflected by a huge genome and a selective transcriptional response to a variety of conditions. We, therefore, hypothesized that exposure of to culture conditions mimicking habitats encountered in the human host might unravel novel antigens that are recognized by melioidosis patients.
METHODS AND RESULTS
In this study, was exposed to various stress and growth conditions, including anaerobiosis, acid stress, oxidative stress, iron starvation and osmotic stress. Immunogenic proteins were identified by probing two-dimensional Western blots of intracellular and extracellular protein extracts with sera from melioidosis patients and controls and subsequent MALDI-TOF MS. Among specific immunogenic signals, 90 % (55/61) of extracellular immunogenic proteins were identified by acid, osmotic or oxidative stress. A total of 84 % (44/52) of intracellular antigens originated from the stationary growth phase, acidic, oxidative and anaerobic conditions. The majority of the extracellular and intracellular protein antigens were identified in only one of the various stress conditions. Sixty-three immunoreactive proteins and an additional 38 candidates from a literature screening were heterologously expressed and subjected to dot blot analysis using melioidosis sera and controls. Our experiments confirmed melioidosis-specific signals in 58 of our immunoproteome candidates. These include 15 antigens with average signal ratios (melioidosis:controls) greater than 10 and another 26 with average ratios greater than 5, including new promising serodiagnostic candidates with a very high signal-to-noise ratio.
CONCLUSION
Our study shows that a comprehensive immunoproteomics approach, using conditions which are likely to be encountered during infection, can identify novel antibody targets previously unrecognized in human melioidosis.
Topics: Humans; Burkholderia pseudomallei; Melioidosis; Antibody Formation; Antigens, Bacterial; Immunoglobulins
PubMed: 38146371
DOI: 10.3389/fimmu.2023.1294113 -
Brazilian Journal of Anesthesiology... 2023Arterial lactate, mixed venous O saturation, venous minus arterial CO partial pressure (PCO) and the ratio between this gradient and the arterial minus venous oxygen...
INTRODUCTION
Arterial lactate, mixed venous O saturation, venous minus arterial CO partial pressure (PCO) and the ratio between this gradient and the arterial minus venous oxygen content (PCO/CO) were proposed as markers of tissue hypoperfusion and oxygenation. The main goals were to characterize the determinants of PCO and PCO/CO, and the interchangeability of the variables calculated from mixed and central venous samples.
METHODS
35 cardiac surgery patients were included. Variables were measured or calculated: after anesthesia induction (T1), end of surgery (T2), and at 6...8.ßhours intervals after ICU admission (T3 and T4).
RESULTS
Macrohemodynamics was characterized by increased cardiac index and low systemic vascular resistances after surgery (p.ß<.ß0.05). Hemoglobin, arterial-pH, lactate, and systemic O metabolism showed significant changes during the study (p.ß<.ß0.05). PCO remained high and without changes, PCO/CO was also high and decreased at T4 (p.ß<.ß0.05). A significant correlation was observed globally and at each time interval, between PCO or PCO/CO with factors that may affect the CO hemoglobin dissociation. A multilevel linear regression model with PCO and PCO/CO as outcome variables showed a significant association for PCO with SO, and BE (p.ß<.ß0.05), while PCO/Ca-vO was significantly associated with Hb, SO, and BE (p.ß<.ß0.05) but not with cardiac output. Measurements and calculations from mixed and central venous blood were not interchangeable.
CONCLUSIONS
PCO and PCO/CO could be influenced by different factors that affect the CO dissociation curve, these variables should be considered with caution in cardiac surgery patients. Finally, central venous and mixed values were not interchangeable.
PubMed: 34407454
DOI: 10.1016/j.bjane.2021.07.025 -
The ISME Journal Dec 2023The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back...
The cycle of life and death and Earth's carbon cycle(s) are intimately linked, yet how bacterial cells, one of the largest pools of biomass on Earth, are recycled back into the carbon cycle remains enigmatic. In particular, no bacteria capable of scavenging dead cells in oxygen-depleted environments have been reported thus far. In this study, we discover the first anaerobes that scavenge dead cells and the two isolated strains use distinct strategies. Based on live-cell imaging, transmission electron microscopy, and hydrolytic enzyme assays, one strain (designated CYCD) relied on cell-to-cell contact and cell invagination for degrading dead food bacteria where as the other strain (MGCD) degraded dead food bacteria via excretion of lytic extracellular enzymes. Both strains could degrade dead cells of differing taxonomy (bacteria and archaea) and differing extents of cell damage, including those without artificially inflicted physical damage. In addition, both depended on symbiotic metabolic interactions for maximizing cell degradation, representing the first cultured syntrophic Bacteroidota. We collectively revealed multiple symbiotic bacterial decomposition routes of dead prokaryotic cells, providing novel insight into the last step of the carbon cycle.
Topics: Anaerobiosis; Bacteria; Bacteria, Anaerobic; Archaea; Environment
PubMed: 37872273
DOI: 10.1038/s41396-023-01538-2 -
Chemosphere Aug 2024Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries... (Review)
Review
Aromatic hydrocarbons like benzene, toluene, xylene, and ethylbenzene (BTEX) can escape into the environment from oil and gas operations and manufacturing industries posing significant health risks to humans and wildlife. Unlike conventional clean-up methods used, biological approaches such as bioremediation can provide a more energy and labour-efficient and environmentally friendly option for sensitive areas such as nature reserves and cities, protecting biodiversity and public health. BTEX contamination is often concentrated in the subsurface of these locations where oxygen is rapidly depleted, and biodegradation relies on anaerobic processes. Thus, it is critical to understand the anaerobic biodegradation characteristics as it has not been explored to a major extent. This review presents novel insights into the degradation mechanisms under anaerobic conditions and presents a detailed description and interconnection between them. BTEX degradation can follow four activation mechanisms: hydroxylation, carboxylation, methylation, and fumarate addition. Hydroxylation is one of the mechanisms that explains the transformation of benzene into phenol, toluene into benzyl alcohol or p-cresol, and ethylbenzene into 1-phenylethanol. Carboxylation to benzoate is thought to be the primary mechanism of degradation for benzene. Despite being poorly understood, benzene methylation has been also reported. Moreover, fumarate addition is the most widely reported mechanism, present in toluene, ethylbenzene, and xylene degradation. Further research efforts are required to better elucidate new and current alternative catabolic pathways. Likewise, a comprehensive analysis of the enzymes involved as well as the development of advance tools such as omic tools can reveal bottlenecks degradation steps and create more effective on-site strategies to address BTEX pollution.
Topics: Biodegradation, Environmental; Anaerobiosis; Benzene Derivatives; Benzene; Toluene; Xylenes; Environmental Pollutants; Hydrocarbons, Aromatic
PubMed: 38821131
DOI: 10.1016/j.chemosphere.2024.142490