Globins Scavenge Sulfur Trioxide Anion Radical

Ordered Motions in the Nitric-Oxide Dioxygenase Mechanism of Flavohemoglobin and Assorted Globins with Tightly Coupled Reductases

Nitric-oxide dioxygenases (NODs) activate and combine O₂ with NO to form nitrate. A variety of oxygen-binding hemoglobins with associated partner reductases or electron donors function as enzymatic NODs. Kinetic and structural investigations of the archetypal two-domain microbial flavohemoglobin-NOD have illuminated an allosteric mechanism that employs selective tunnels for O₂ and NO, gates for NO and nitrate, transient O₂ association with ferric heme, and an O₂ and NO-triggered, ferric heme spin crossover-driven, motion-controlled, and dipole-regulated electron-transfer switch. The proposed mechanism facilitates radical-radical coupling of ferric-superoxide with NO to form nitrate while preventing suicidal ferrous-NO formation. Diverse globins display the structural and functional motifs necessary for a similar allosteric NOD mechanism. In silico docking simulations reveal monomeric erythrocyte hemoglobin alpha-chain and beta-chain intrinsically matched and tightly coupled with NADH-cytochrome b₅ oxidoreductase and NADPH-cytochrome P450 oxidoreductase, respectively, forming membrane-bound flavohemoglobin-like mammalian NODs. The neuroprotective neuroglobin manifests a potential NOD role in a close-fitting ternary complex with membrane-bound NADH-cytochrome b₅ oxidoreductase and cytochrome b₅. Cytoglobin interfaces weakly with cytochrome b₅ for O₂ and NO-regulated electron-transfer and coupled NOD activity. The mechanistic model also provides insight into the evolution of O₂ binding cooperativity in hemoglobin and a basis for the discovery of allosteric NOD inhibitors.

Neuroglobin, clues to function and mechanism

Neuroglobin is expressed in vertebrate brain and belongs to a branch of the globin family that diverged early in evolution. Sequence conservation and presence in nervous cells of several taxa suggests a relevant role in the nervous system, with tight structural restraints. Twenty years after its discovery, a rich scientific literature provides convincing evidence of the involvement of neuroglobin in sustaining neuron viability in physiological and pathological conditions however, a full and conclusive picture of its specific function, or set of functions is still lacking. The difficulty of unambiguously assigning a precise mechanism and biochemical role to neuroglobin might arise from the participation to one or more cell mechanism that redundantly guarantee the functioning of the highly specialized and metabolically demanding central nervous system of vertebrates. Here we collect findings and hypotheses arising from recent biochemical, biophysical, structural, in cell and in vivo experimental work on neuroglobin, aiming at providing an overview of the most recent literature. Proteins are said to have jobs and hobbies, it is possible that, in the case of neuroglobin, evolution has selected for it more than one job, and support to cover for its occasional failings. Disentangling the mechanisms and roles of neuroglobin is thus a challenging task that might be achieved by considering data from different disciplines and experimental approaches.

Structural and (Pseudo-)Enzymatic Properties of Neuroglobin: Its Possible Role in Neuroprotection

Neuroglobin (Ngb), the third member of the globin family, was discovered in human and murine brains in 2000. This monomeric globin is structurally similar to myoglobin (Mb) and hemoglobin (Hb) α and β subunits, but it hosts a bis-histidyl six-coordinated heme-Fe atom. Therefore, the heme-based reactivity of Ngb is modulated by the dissociation of the distal HisE7-heme-Fe bond, which reflects in turn the redox state of the cell. The high Ngb levels (~100–200 μM) present in the retinal ganglion cell layer and in the optic nerve facilitate the O₂ buffer and delivery. In contrast, the very low levels of Ngb (~1 μM) in most tissues and organs support (pseudo-)enzymatic properties including NO/O₂ metabolism, peroxynitrite and free radical scavenging, nitrite, hydroxylamine, hydrogen sulfide reduction, and the nitration of aromatic compounds. Here, structural and (pseudo-)enzymatic properties of Ngb, which are at the root of tissue and organ protection, are reviewed, envisaging a possible role in the protection from neuronal degeneration of the retina and the optic nerve.

Sodium sulfite causes gastric mucosal cell death by inducing oxidative stress

Sulfites are commonly used as a preservative and antioxidant additives in the food industry. Sulfites are absorbed by the gastrointestinal tract and distributed essentially to all body tissues. Although sulfites have been believed to be safe food additives, some studies have shown that they exhibit adverse effects in various tissues. In this study, we examined the cytotoxic effect of sodium sulfite (Na₂SO₃) against rat gastric mucosal cells (RGM1) and further investigated its underlying molecular mechanism. We demonstrated that exposure to Na₂SO₃ exerts significant cytotoxicity in RGM1 cells through induction of oxidative stress. Exposure of RGM1 cells to Na₂SO₃ caused a significant formation of protein carbonyls and 8-hydroxy-2'-deoxyguanosine, major oxidative stress markers, with a concomitant accumulation of carbonylated protein-related aggregates. Furthermore, we found that incubation of lysozyme with Na₂SO₃ evokes protein carbonylation and aggregation via the metal ion-catalyzed free radical formation derived from Na₂SO₃. Our results suggest that Na₂SO₃ might lead to gastric tissue injury via induction of oxidative stress by the formation of Na₂SO₃-related free radicals.

A novel combination of sodium metabisulfite and a chemical mixture based on sodium benzoate, potassium sorbate, and sodium nitrite for aerobic preservation of fruit and vegetable discards and lactic acid fermentation in a total mixed ration for ruminants

Objective

Our recent findings confirmed the effectiveness of sodium metabisulfite (SMB) in controlling the growth of undesirable microorganisms in fruit and vegetable discards (FVD); however, lactic acid bacteria (LAB) are susceptible to its antibacterial effects. Two series of experiments were conducted to enable the survivability of LAB during silage fermentation of a total mixed ration (TMR) containing SMB-treated FVD.

Methods

In Exp. 1, the objective was to isolate a strain of LAB tolerable to the toxic effect of SMB. In Exp. 2, the SMB load was minimized through its partial replacement with a chemical mixture (CM) based on sodium benzoate (57%), potassium sorbate (29%), and sodium nitrite (14%). FVD was treated with SMB + CM (2 g each/kg biomass) and added to the TMR at varying levels (0%, 10%, or 20%), with or without KU18 inoculation.

Results

The KU18 was screened as a presumptive LAB strain showing superior tolerance to SMB in broth medium, and was identified at the molecular level using 16S rRNA gene sequence analysis as Lactobacillus plantarum. Inoculation of KU18 in TMR containing SMB was not successful for the LAB development, biomass acidification, and organoleptic properties of the resultant silage. In Exp. 2, based on the effectiveness and economic considerations, an equal proportion of SMB and CM (2 g each/kg FVD) was selected as the optimal loads for the subsequent silage fermentation experiment. Slight differences were determined in LAB development, biomass acidification, and sensorial characteristics among the experimental silages, suggesting the low toxicity of the preservatives on LAB growth.

Conclusion

Although KU18 strain was not able to efficiently develop in silage mass containing SMB-treated FVD, the partial substitution of SMB load with the CM effectively alleviated the toxic effect of SMB and allowed LAB development during the fermentation of SMB + CM-treated FVD in TMR.

Allostery in the nitric oxide dioxygenase mechanism of flavohemoglobin

The substrates O₂ and NO cooperatively activate the NO dioxygenase function of Escherichia coli flavohemoglobin. Steady-state and transient kinetic measurements support a structure-based mechanistic model in which O₂ and NO movements and conserved amino acids at the E11, G8, E2, E7, B10, and F7 positions within the globin domain control activation. In the cooperative and allosteric mechanism, O₂ migrates to the catalytic heme site via a long hydrophobic tunnel and displaces LeuE11 away from the ferric iron, which forces open a short tunnel to the catalytic site gated by the ValG8/IleE15 pair and LeuE11. NO permeates this tunnel and leverages upon the gating side chains triggering the CD loop to furl, which moves the E and F-helices and switches an electron transfer gate formed by LysF7, GlnE7, and water. This allows FADH₂ to reduce the ferric iron, which forms the stable ferric–superoxide–TyrB10/GlnE7 complex. This complex reacts with internalized NO with a bimolecular rate constant of 10¹⁰ M⁻¹ s⁻¹ forming nitrate, which migrates to the CD loop and unfurls the spring-like structure. To restart the cycle, LeuE11 toggles back to the ferric iron. Actuating electron transfer with O₂ and NO movements averts irreversible NO poisoning and reductive inactivation of the enzyme. Together, structure snapshots and kinetic constants provide glimpses of intermediate conformational states, time scales for motion, and associated energies.

Long Chain Fatty Acid Degradation Coupled to Biological Sulfidogenesis: A Prospect for Enhanced Metal Recovery

This research assessed the microbiological suitability of oleate degradation coupled to sulfidogenesis by enriching communities from anaerobic sludge treating dairy products with S⁰, SO 3 2 - , SO 4 2 - , and S₂ O 3 2 - as electron acceptors. The limiting factor hampering highly efficient oleate degradation was investigated in batch reactors. The best sulfidogenic performance coupled to specialization of the enriched bacterial community was obtained for S⁰- and S₂ O 3 2 - -reducing enrichments, with 15.6 (± 0.2) and 9.0 (± 0.0) mM of sulfide production, respectively. Microbial community analyses revealed predominance of Enterobacteraceae (50.6 ± 5.7%), Sulfurospirillum (23.1 ± 0.1%), Bacteroides (7.5 ± 1.5%) and Seleniivibrio (6.9 ± 1.1%) in S⁰-reducing cultures. In S₂ O 3 2 - -reducing enrichments, the genus Desulfurella predominated (49.2 ± 1.2%), followed by the Enterobacterales order (20.9 ± 2.3%). S⁰-reducing cultures were not affected by oleate concentrations up to 5 mM, while S₂ O 3 2 - -reducing cultures could degrade oleate in concentrations up to 10 mM, with no significant impact on sulfidogenesis. In sequencing batch reactors operated with sulfide stripping, the S⁰-reducing enrichment produced 145.8 mM sulfide, precipitating Zn as ZnS in a separate tank. The S₂ O 3 2 - fed bioreactor only produced 23.4 mM of sulfide precipitated as ZnS. The lower sulfide production likely happened due to sulfite toxicity, an intermediate of thiosulfate reduction. Therefore, elemental sulfur reduction represents an excellent alternative to the currently adopted approaches for LCFA degradation. To the best of our knowledge, this is the first report of oleate degradation with the flux of electrons totally diverted toward sulfide production for metal precipitation, showing great efficiency of LCFA degradation coupled to high levels of metals precipitated as metal sulfide.

Flavohaemoglobin: the pre-eminent nitric oxide-detoxifying machine of microorganisms

Flavohaemoglobins were first described in yeast as early as the 1970s but their functions were unclear. The surge in interest in nitric oxide biology and both serendipitous and hypothesis-driven discoveries in bacterial systems have transformed our understanding of this unusual two-domain globin into a comprehensive, yet undoubtedly incomplete, appreciation of its pre-eminent role in nitric oxide detoxification. Here, I focus on research on the flavohaemoglobins of microorganisms, especially of bacteria, and update several earlier and more comprehensive reviews, emphasising advances over the past 5 to 10 years and some controversies that have arisen. Inevitably, in light of space restrictions, details of nitric oxide metabolism and globins in higher organisms are brief.

Long Chain Fatty Acid Degradation Coupled to Biological Sulfidogenesis: A Prospect for Enhanced Metal Recovery

This research assessed the microbiological suitability of oleate degradation coupled to sulfidogenesis by enriching communities from anaerobic sludge treating dairy products with S⁰, SO 3 2 - , SO 4 2 - , and S₂ O 3 2 - as electron acceptors. The limiting factor hampering highly efficient oleate degradation was investigated in batch reactors. The best sulfidogenic performance coupled to specialization of the enriched bacterial community was obtained for S⁰- and S₂ O 3 2 - -reducing enrichments, with 15.6 (± 0.2) and 9.0 (± 0.0) mM of sulfide production, respectively. Microbial community analyses revealed predominance of Enterobacteraceae (50.6 ± 5.7%), Sulfurospirillum (23.1 ± 0.1%), Bacteroides (7.5 ± 1.5%) and Seleniivibrio (6.9 ± 1.1%) in S⁰-reducing cultures. In S₂ O 3 2 - -reducing enrichments, the genus Desulfurella predominated (49.2 ± 1.2%), followed by the Enterobacterales order (20.9 ± 2.3%). S⁰-reducing cultures were not affected by oleate concentrations up to 5 mM, while S₂ O 3 2 - -reducing cultures could degrade oleate in concentrations up to 10 mM, with no significant impact on sulfidogenesis. In sequencing batch reactors operated with sulfide stripping, the S⁰-reducing enrichment produced 145.8 mM sulfide, precipitating Zn as ZnS in a separate tank. The S₂ O 3 2 - fed bioreactor only produced 23.4 mM of sulfide precipitated as ZnS. The lower sulfide production likely happened due to sulfite toxicity, an intermediate of thiosulfate reduction. Therefore, elemental sulfur reduction represents an excellent alternative to the currently adopted approaches for LCFA degradation. To the best of our knowledge, this is the first report of oleate degradation with the flux of electrons totally diverted toward sulfide production for metal precipitation, showing great efficiency of LCFA degradation coupled to high levels of metals precipitated as metal sulfide.

Redox-Driven Signaling: 2-Oxo Acid Dehydrogenase Complexes as Sensors and Transmitters of Metabolic Imbalance

SIGNIFICANCE

This article develops a holistic view on production of reactive oxygen species (ROS) by 2-oxo acid dehydrogenase complexes. Recent Advances: Catalytic and structural properties of the complexes and their components evolved to minimize damaging effects of side reactions, including ROS generation, simultaneously exploiting the reactions for homeostatic signaling.

CRITICAL ISSUES

Side reactions of the complexes, characterized in vitro, are analyzed in view of protein interactions and conditions in vivo. Quantitative data support prevalence of the forward 2-oxo acid oxidation over the backward NADH oxidation in feeding physiologically significant ROS production by the complexes. Special focus on interactions between the active sites within 2-oxo acid dehydrogenase complexes highlights the central relevance of the complex-bound thiyl radicals in regulation of and signaling by complex-generated ROS. The thiyl radicals arise when dihydrolipoyl residues of the complexes regenerate FADH₂ from the flavin semiquinone coproduced with superoxide anion radical in 1e^- oxidation of FADH₂ by molecular oxygen.

FUTURE DIRECTIONS

Interaction of 2-oxo acid dehydrogenase complexes with thioredoxins (TRXs), peroxiredoxins, and glutaredoxins mediates scavenging of the thiyl radicals and ROS generated by the complexes, underlying signaling of disproportional availability of 2-oxo acids, CoA, and NAD⁺ in key metabolic branch points through thiol/disulfide exchange and medically important hypoxia-inducible factor, mammalian target of rapamycin (mTOR), poly (ADP-ribose) polymerase, and sirtuins. High reactivity of the coproduced ROS and thiyl radicals to iron/sulfur clusters and nitric oxide, peroxynitrite reductase activity of peroxiredoxins and transnitrosylating function of thioredoxin, implicate the side reactions of 2-oxo acid dehydrogenase complexes in nitric oxide-dependent signaling and damage.

Long-term anaerobic conservation of fruit and vegetable discards without or with moisture adjustment after aerobic preservation with sodium metabisulfite

The high moisture and soluble carbohydrates contents of fruit and vegetable discards accelerate putrefaction; thus, the immediate use of preservatives is necessary to prevent their decay and allow further use. Two series of experiments were performed to evaluate the conservation stability of fruit and vegetable discards through ensiling. Fruit and vegetable discards were not treated or treated with 6 g sodium metabisulfite/kg fruit and vegetable discards and aerobically challenged for 7 days. In Experiment 1, sodium metabisulfite-treated fruit and vegetable discards were ensiled alone as high-moisture biomass. Silage fermentation was not effective in preventing the deterioration and mold control, which resulted in the rapid depletion of sugars and dry matter loss in control silage (without sodium metabisulfite). Conversely, the low number of undesirable microorganisms resulted in the negligible loss of nutrients in the sodium metabisulfite-treated silage. In Experiment 2, sodium metabisulfite-treated fruit and vegetable discards were co-ensiled with dry by-product feeds at varying proportions to provide sodium metabisulfite loads of 1.6, 2.4, 3.2, and 4 g/kg biomass. Based on microbiological, nutrient composition, and organoleptic evaluations, the sodium metabisulfite load of 3.2 g/kg biomass provided the most desirable conservation parameters. This study provides a clean route to the safe utilization of the discards for a prolonged period, with negligible dry matter and nutrient loss.

Nitric oxide prevents Aft1 activation and metabolic remodeling in frataxin-deficient yeast

Yeast frataxin homolog (Yfh1) is the orthologue of human frataxin, a mitochondrial protein whose deficiency causes Friedreich Ataxia. Yfh1 deficiency activates Aft1, a transcription factor governing iron homeostasis in yeast cells. Although the mechanisms causing this activation are not completely understood, it is assumed that it may be caused by iron-sulfur deficiency. However, several evidences indicate that activation of Aft1 occurs in the absence of iron-sulfur deficiency. Besides, Yfh1 deficiency also leads to metabolic remodeling (mainly consisting in a shift from respiratory to fermentative metabolism) and to induction of Yhb1, a nitric oxide (NO) detoxifying enzyme. In this work, we have used conditional Yfh1 mutant yeast strains to investigate the relationship between NO, Aft1 activation and metabolic remodeling. We have observed that NO prevents Aft1 activation caused by Yfh1 deficiency. This phenomenon is not observed when Aft1 is activated by iron scarcity or impaired iron-sulfur biogenesis. In addition, analyzing key metabolic proteins by a targeted proteomics approach, we have observed that NO prevents the metabolic remodeling caused by Yfh1 deficiency. We conclude that Aft1 activation in Yfh1-deficient yeasts is not caused by iron-sulfur deficiency or iron scarcity. Our hypothesis is that Yfh1 deficiency leads to the presence of anomalous iron species that can compromise iron bioavailability and activate a signaling cascade that results in Aft1 activation and metabolic remodeling.

Sulfites inhibit the growth of four species of beneficial gut bacteria at concentrations regarded as safe for food

Sulfites and other preservatives are considered food additives to limit bacterial contamination, and are generally regarded as safe for consumption by governmental regulatory agencies at concentrations up to 5000 parts per million (ppm). Consumption of bactericidal and bacteriostatic drugs have been shown to damage beneficial bacteria in the human gut and this damage has been associated with several diseases. In the present study, bactericidal and bacteriostatic effects of two common food preservatives, sodium bisulfite and sodium sulfite, were tested on four known beneficial bacterial species common as probiotics and members of the human gut microbiota. Lactobacillus species casei, plantarum and rhamnosus, and Streptococcus thermophilus were grown under optimal environmental conditions to achieve early log phase at start of experiments. Bacterial cultures were challenged with sulfite concentrations ranging between 10 and 3780 ppm for six hours. To establish a control, a culture of each species was inoculated into media containing no sulfite preservative. By two hours of exposure, a substantial decrease (or no increase) of cell numbers (based on OD₆₀₀ readings) were observed for all bacteria types, in concentrations of sulfites between 250–500 ppm, compared to cells in sulfite free media. Further testing using serial dilution and drop plates identified bactericidal effects in concentrations ranging between 1000–3780 ppm on all the Lactobacillus species by 4 hours of exposure and bactericidal effects on S. thermophilus in 2000ppm NaHSO₃ after 6 hours of exposure.