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PubMed2026

Viral communities from long-term anaerobic alkane-oxidizing enrichment cultures encode predicted cell surface adhesion functions.

The anaerobic oxidation of methane and C2+-alkanes is a dominant metabolism within hydrocarbon-rich deep-sea sediments and is largely mediated by alkane-oxidizing archaea in metabolic partnership with syntrophic sulfate-reducing bacteria. Although these processes fuel a diverse ecosystem, the viral component of alkane-rich sediments has historically been overlooked. We analyzed the viral assemblages in long-term sediment-free cultures of alkane-degrading organisms and found that abiotic factors such as incubation temperature had a greater correlation with community composition than with the phylogenetic patterns among individual viral species. No auxiliary metabolic genes (AMGs) directly involved in hydrocarbon oxidation or sulfate reduction were found, but the presence of candidate AMGs involved in heme synthesis pathways common in methane oxidizers hints at a possible viral impact on alkane degradation. We also examined potential host-virus pairs using CRISPR- and tRNA-based methods. Lastly, we identified the presence of nosD-like proteins in viruses from sediment-derived systems that are not present in water column datasets; their distribution, genomic context, and lack of canonical nosD characteristics suggest an alternate adhesion-related role in sediment communities. The number of new viruses obtained from these multi-year enrichment cultures and their potential roles in mediating host physiology illustrate the importance of studying the viral component in laboratory and environmental systems.

Geologic Sediments↗
PubMed2026

Symbiosis reshapes metabolism of sulfate-reducing bacteria in gutless marine worms.

Sulfate-reducing bacteria (SRB) are widespread in marine and terrestrial environments, where they often form syntrophic associations with bacteria, archaea, and eukaryotes. Among the most intimate of these are multipartite symbioses in gutless marine oligochaete worms, which host SRB and sulfur-oxidizing endosymbionts that engage in a syntrophic exchange of sulfur compounds. Despite decades of research on free-living SRB, the metabolic traits that enable SRB to persist in symbiosis, and how these differ across hosts and environments, remain poorly understood. We show that a globally distributed clade of symbiotic SRB, which we named Candidatus Desulfoconcordia, has a conserved core metabolism that diverges from free-living relatives. Using comparative genomics and metaproteomics, we reveal that these endosymbionts retain key traits of SRB such as sulfate reduction, complete oxidation of acetate to CO2, amino acid degradation for nitrogen acquisition, and transport of essential nutrients. However, they exhibit a more oxygen-tolerant metabolism and lack typical nutrient-scavenging mechanisms of free-living SRB. One trait, the glyoxylate bypass, was consistently expressed in situ and may serve both in reactive oxygen species defence and in biomass generation. The expression of oxygen-tolerant pathways, coupled with the loss of nutrient-scavenging functions, indicate specialization to a host-associated, redox-fluctuating environment distinct from that of free-living SRB. The symbiont genomes are also larger than those of free-living relatives, contrasting with genome reduction in many endosymbionts and reinforcing the importance of metabolic versatility. Our findings provide a framework for understanding how metabolic flexibility enables SRB to persist in long-term multipartite symbioses across diverse marine ecosystems.

Symbiosis↗
PubMed1975

Fatty acid and ketone body metabolism in the rat: response to diet and exercise.

This study was designed to measure the response of key enzymes of ketone body metabolism in heart, skeletal muscle, and liver to diet and exercise, two conditions known to influence ketone body utilization. A 3 (diet: control, high fat, or high carbohydrate) X 2 (kill condition: rested or exhausted) X 2 (training: trained or untrained) factorial design was used to estimate main experimental effects as well as identify significant interactions of the variables. Physical training (treadmill running) was associated with a doubling of the activity of skeletal muscle 3-oxoacid CoA transferase, a key enzyme in extrahepatic ketone body utilization. The activity of the rate-limiting enzyme of liver ketone body production, hydroxymethylglutaryl CoA synthetase (HMG CoA synthetase), was not greatly influenced by training or exhuastive exercise indicating that the metabolic control of the ketosis of exercise may more likely be a function of the supply of fatty acids to the liver rather than the activity of HMG CoA synthetase. Feeding a high fat diet, on the other hand, significantly increased the activity of liver HMG CoA synthetase, indicating that the ketosis of fat feeding may be of a different nature than that of exercise. The results of this study indicate that physical training is associated with biochemical adaptations in ketone body metabolism as well as fatty acid oxidation, and that trained individuals are metabolically better endowed to benefit from the ketosis of exercise than untrained individuals.

Acetyl-CoA C-Acetyltransferase↗
PubMed1975

Oxidation of carbon monoxide and methane by Pseudomonas methanica.

The oxidation of carbon monoxide and methane by suspensions and ultrasonic extracts of Pseudomonas methanica was studied. A continuous assay for the oxidation of CO to CO2 was devised, using O2 and CO2 electrodes in combination. Stoicheiometries of CO-dependent CO2 formation, O2 consumption and NADH oxidation, and the partial stoicheiometries of methane-dependent NADH oxidation, suggest the involvement of a mono-oxygenase in these oxidations. Evidence is presented suggesting methane and CO oxidation are catalysed by a single enzyme system, distinct, at least in part, from the NADH oxidase present in extracts. Ethanol was able to provide the reductant necessary for CO oxidation by cell suspensions, though the metabolism of ethanol by P. methanica was found unlikely to result in substrate-level formation of NADH; the means whereby alcohol oxidation could supply reductant for the mono-oxygenase are discussed.

Ammonium Chloride↗
PubMed2026

Cobalt starvation affects multiple cellular processes in Desulfofundulus kuznetsovii TPOSR during alcohol oxidation.

Cobalt influences the methanol metabolism of Desulfofundulus kuznetsovii TPOSR, specifically by modulating the activity of one of its alcohol dehydrogenases (ADH), Adh1. However, the effects of cobalt on the broader proteome of strain TPOSR, as well as the utilization of alcohols besides methanol, remain unexplored. Here, proteomic analyses of strain TPOSR grown with and without cobalt on different alcohol substrates show that cobalt starvation impacts multiple cellular processes, including cobalamin biosynthesis, iron-sulphur cluster assembly and, most prominently, energy metabolism as indicated by altered abundances of hydrogenases and NAD(P)-dependent oxidoreductases. Despite the presence of six ADH-encoding genes in the genome, Adh1 is the dominant ADH during growth not only on methanol but also on several primary alcohols and diols (ethanol, 1-propanol, 1,2-propanediol, 1,3-propanediol, butanol, pentanol and heptanol). Enzymatic assays with purified Adh1 confirm activity with these substrates, except 1,3-propanediol, and show no activity toward secondary alcohols (2-propanol and 2-butanol). Comparative proteomics analyses of other sulphate-reducing microorganisms (SRMs), namely Desulfofundulus australicum and Solidesulfovibrio carbinolicus, further indicate that methanol and ethanol oxidation in SRMs is mediated by a single ADH/AOR pair. Together, these findings highlight the central role of cobalt in alcohol metabolism in strain TPOSR and identify conserved ADH/AOR enzymes as promising candidates for biotechnological applications.

Cobalt↗
PubMed1975

Hydroxylation of p-Coumaric acid by illuminated chloroplasts. The role of superoxide.

1. Chloroplasts isolated from leaves of spinach-beet (Beta vulgaris L. ssp. vulgaris) do not catalyse the hydroxylation of p-coumaric acid in the dark unless a reductant (such as ascorbate, NADH or NADPH) is added. Superoxide dismutase has no effect on this reaction. 2. Illuminated chloroplasts catalyse the hydroxylation in the absence of added reductant. This reaction is completely inhibited by superoxide dismutase, but catalase has little effect. 3. Both hydroxylation in the light and hydroxylation in the dark in the presence of reductants are inhibited by diethyldithiocarbamate, EDTA, cyanide and 2-mercaptoethanol. 4. It is proposed that O-2- generated by illuminated chloroplasts is involved in the provision of a reductant to the enzyme phenolase.

Ascorbic Acid↗
PubMed1975

The renaturation of reduced polyalanyl-chymotrypsinogen and chymotrypsinogen.

Chymotrypsinogen has been successfully renatured in solution, after reduction of its 5 disulfide bonds in 6 M guanidine-HCl. This has been made possible by the study of the renaturation of a model derivative, polyalanyl-chymotrypsinogen. The reduced derivative is shown to refold and reoxodize spontaneously, with a 30-40% yield, into molecules which are monomeric and fully susceptible to activation by trypsin. Chymotrypsinogen can also be renatured but only in the presence of reagents allowing disulfide interchange and of moderate concentrations of guanidine-HCl or urea. These results illustrate how the kinetic trapping of incorrectly folded molecules by wrong S-S bonds and aggregation can be overcome, thus allowing the correct refolding of the protein.

Alanine↗
PubMed1976

Hydrogen-isotope exchange of oxidized and reduced cytochrome c. A comparison of mass spectrometry and infrared methods.

Hydrogen-deuterium exchange in 2H20 solutions of the two redox states of horse heart cytochrome c was investigated at 20 degrees C, pH 7, by mass spectrometry and infrared spectroscopy. Mass spectrometry indicates that ferricytochrome has 20 hydrogens unexchanged after 24 h, 28 hydrogens exchanging between 10 min and 24 h, and 156 hydrogens exchanging within 10 min; comparative values for ferrocytochrome are 45, 19 and 140. The displacement of the exchange curves obtained by infrared corresponds to 8 to 9 peptide hydrogens. These combined methods show many non-peptide hydrogens exchanging rapidly (87 and 79 for ferricytochrome c and ferrocytochrome c respectively), whereas others, probably buried inside the molecule and involved in hydrogen bonds, are not exchanged, even after 24 h (14 and 30 hydrogens respectively, which is relatively large for a small protein). Infrared results are given in terms of changes of standard free energy for the transconformational reaction which exposes the peptide hydrogens to solvent: in ferricytochrome c and ferrycoytochrome c, 30% and 40% respectively of the peptide hydrogens are protected by conformational transitions stabilized by more than 5 kcal/mol (21 kJ/mol), which implies a large increase in rigidity for the reduced form.

Animals↗
PubMed1976

Bacterial metabolism of resorcinylic compounds: purification and properties of orcinol hydroxylase and resorcinol hydroxylase from Pseudomonas putida ORC.

The hydroxylase activities observed in extracts of Pseudomonas putida ORC after growth on orcinol and resorcinol as sole source of carbon have been purified to homogeneity. Both enzymes were shown to be flavoproteins and to contain approximately 1 mol of FAD for each polypeptide chain, S20,W values for each enzyme are 4.1 +/- 0.1 and are independent of the presence of their aromatic substrates. Molecular weight determinations under native (approximately 68000) and denaturing (approximately 70000) conditions indicated that they are monomeric. The visible absorption spectra identical but the circular dichroic spectra of the two proteins can be distinguished. Although each protein catalyzes the NAD(P)H and O2-dependent hydroxylation of both orcinol and resorcinol, the efficiency of the transformations of the substrates by the two enzymes is radically different; furthermore resorcinol hydroxylase is much more versatile in the aromatic compounds it can utilize as substrates and effectors. Other properties of the enzymes which clearly establish their own identity include their serological characteristics and amino acid composition; the latter property is particularly evident when the quantities of valine and alanine residues are compared. The synthesis of each enzyme is also under different regulatory constraints, being controlled by the substrate used for growth.

Amino Acids↗
PubMed1975

A study of the human metabolism of secbutobarbitone.

The urinary excretion of secbutobarbitone (I) and its metabolites has been studied quantitatively using combined gas chromatography-mass spectrometry. After a single oral dose was given to healthy male volunteers, unchanged drug (5-9%), 2'-hydroxysecbutobarbitone (II, 1.7-3.2%), 2'-oxosecbutobarbitone (III, less than 1%), and the carboxylic acid (IV, 24-34%) were found. The kinetics of the excretion process were studied.

Barbiturates↗
PubMed2025

The Role of the [2Fe-2S] Cluster of Escherichia coli IscR in Responding to Redox-Cycling Agents.

The mechanisms by which cells respond to growth inhibitory redox-cycling agents is only partially understood. In Escherichia coli K12, the IscR regulon, which includes the ISC and SUF Fe-S cluster biogenesis machineries, is differentially expressed in response to these agents. Here, we report how one redox-cycling agent, phenazine methosulfate (PMS), regulates IscR activity via its [2Fe-2S] cluster cofactor. A direct role for IscR in mediating the response to PMS was inferred from the PMS-dependent weakening of [2Fe-2S]-IscR binding to an isc operon type 1 DNA site in vitro. This decrease in DNA binding was attributed to the accompanying oxidation of its [2Fe-2S]1+ cluster. Exposure of anaerobic cultures to PMS leads to increased isc expression, as expected from IscR cluster oxidation and impaired binding to type 1 sites in the isc promoter. However, this same anaerobic PMS treatment did not change expression of type 2 site promoters, such as suf, which require IscR that lacks an Fe-S cluster (apo-IscR) for effective transcriptional regulation. In contrast, PMS exposure under aerobic conditions significantly increased both isc and suf expression, indicating the formation of both [2Fe-2S]2+-IscR and apo-IscR. This effect was partially attributed to superoxide generation by PMS under aerobic conditions, as evidenced by a superoxide dismutase-deficient mutant showing a modest impact on isc and suf expression. Together, these findings provide new insights into redox-cycling dependent regulation of IscR activity and highlight the distinct activities of apo-IscR, [2Fe-2S]2+-IscR and [2Fe-2S]1+-IscR in controlling the IscR regulon.

Escherichia coli Proteins↗
PubMed2026

Strict Aerobic Lifestyle and Anaerobic Survival of Bacteria: Inseparable Twins?

For many decades the existence of strict aerobic bacteria was part of every textbook. However, considering habitats like soils or surfaces, many of these microorganisms are exposed to drastic changes in oxygen tension. A simple rain shower can change oxygen diffusion rates by a factor of 10.000. Thus, for many of the so-called strict aerobic bacteria, anaerobic growth and survival strategies were discovered, mainly relying on the use of alternative electron acceptors to oxygen, redox-active metabolites, or fermentation processes generating ATP at the substrate level. Survival without growth was recognized as an important lifestyle of bacteria. With the increasing availability of genome data, many highly diverse growth and survival strategies have become apparent in bacteria. But the overall picture is far from complete. Only recently, a novel puzzle piece of the anaerobic survival strategy of the opportunistic pathogen and model bacterium Pseudomonas aeruginosa in the absence of alternative electron acceptors was elucidated. It relies on the re-wiring of carbon flux away from the Entner-Doudoroff pathway towards the pentose-phosphate pathway and use of a phosphoketolase to allow for metabolic flux while preventing nonproductive NADH formation under these fermentation conditions and for ATP generation via acetate kinase.

Anaerobiosis↗
PubMed2025

N-glycan remodeling by α-D-mannosidase and β-D-N-acetylhexosaminidase regulates fruit softening, redox balance, and post-harvest pathogen resistance.

Post-harvest loss of fruits and vegetables poses significant challenges to food security and economic sustainability, primarily due to ripening-associated excessive softening that shortens shelf life and increases susceptibility to pathogens. N-glycans, N-glycoproteins, and their processing enzymes are integral to various plant processes, including fruit ripening. Among these, α-D-mannosidase (α-Man) and β-D-N-acetylhexosaminidase (β-Hex) are key ripening-specific enzymes that modulate fruit softening. Previously, we have shown that RNAi-mediated suppression of α-Man or β-Hex improves fruit shelf life and firmness in both climacteric and non-climacteric fruits. However, the underlying molecular and biochemical basis of fruit softening regulation by α-Man and β-Hex was not well understood. In this study, we developed transgenic tomato (Solanum lycopersicum) plants by silencing α-Man and β-Hex simultaneously using RNAi. Suppression of these enzymes reduces N-glycoprotein degradation, downregulates pectin dissolution, and inhibits ripening-related gene expression. RNAi fruits exhibited enhanced shelf life, greater firmness, reduced reactive oxygen species (ROS) accumulation and increased resistance against post-harvest pathogens without affecting plant growth, fruit development, yield, or nutritional quality. To further explore the molecular mechanism of α-Man and β-Hex function, we purified and quantified N-glycans in RNAi fruits and other ripening-impaired mutants, identifying key N-glycan species. We also carried out iTRAQ-based quantitative proteome profiling to investigate the abundance of proteins in ripened fruit affected by silencing of α-Man and β-Hex. Molecular insights revealed that N-glycan processing and degradation are key events during ripening, influencing cell wall softening, fruit redox state, and post-harvest quality attributes. This study highlights the potential of co-silencing α-Man and β-Hex as a novel approach to extending the shelf life of fruits, regardless of their climacteric behavior, without compromising quality or yield.

Fruit↗
PubMed2025

Myo-inositol is a key regulator of avian metabolism: From mechanisms to seasonal behavior.

Being naturally hyperglycemic and insulin insensitive, birds maintain plasma glucose levels twice as high as mammals of similar size. Recent evidence suggests that perturbation of myo-inositol (MI) plays a role in mammalian hyperglycemic regulation. Using an integrative approach, we identify a fundamental role of MI in avian metabolism. We show that MI transporters are highly conserved across birds and that dietary MI reduces fat accumulation in Anna's hummingbirds. MI consumption by hummingbirds varies with seasonal changes in body mass, consistent with a regulatory role. Furthermore, MI enhances fatty acid oxidation in avian cells, via effects on pyruvate-dehydrogenase complexes, indicating a role in mitochondrial fuel selection. Our findings underscore the importance of MI in avian metabolism, offering insights into their evolutionary adaptations in the context of insulin insensitivity.

Animals↗
PubMed2026

Tumor-derived antioxidants suppress immunity by depriving T cells of reactive oxygen species.

Reactive oxygen species (ROS) promote genomic instability and fuel oncogenic signaling in cancer, but antioxidant therapies have so far failed to improve, or worsen, cancer outcomes. Emerging data suggest that T cells depend on ROS for signal transduction. In this study, we show that tumors exploit this dependency, releasing antioxidant enzymes into the tumor environment to suppress T cell-mediated antitumor immunity. The interstitial fluid of tumors possesses potent antioxidant activity, associated with enrichment of the antioxidant enzyme peroxiredoxin 1 (PRDX1). Extracellular PRDX1 deprives T cells of ROS, preventing oxidative inactivation of phosphatases required for T cell receptor-driven kinase signaling and effector function. Prdx1 is up-regulated upon cancer immunoediting, and loss of PRDX1 within tumors enhances antitumor immunity and immunotherapy responses. These findings define a redox-dependent mechanism of tumor immunosuppression that is potentially amenable to therapeutic intervention.

Animals↗