What are the sources of hydrogen peroxide production by heart mitochondria?

Coupled rat heart mitochondria produce externally hydrogen peroxide at the rates which correspond to about 0.8 and 0.3% of the total oxygen consumption at State 4 with succinate and glutamate plus malate as the respiratory substrates, respectively. Stimulation of the respiratory activities by ADP (State 4–State 3 transition) decreases the succinate- and glutamate plus malate-supported H₂O₂ production 8- and 1.3-times, respectively. NH₄⁺ strongly stimulates hydrogen peroxide formation with either substrate without any effect on State 4 and/or State 3 respiration. Rotenone-treated, alamethicin-permeabilized mitochondria catalyze NADH-supported H₂O₂ production at a rate about 10-fold higher than that seen in intact mitochondria under optimal (State 4 succinate-supported respiration in the presence of ammonium chloride) conditions. NADH-supported hydrogen peroxide production by the rotenone-treated mitochondria devoid of a permeability barrier for H₂O₂ diffusion by alamethicin treatment are only partially (～ 50%) sensitive to the Complex I NADH binding site-specific inhibitor, NADH-OH. The residual activity is strongly (～ 6-fold) stimulated by ammonium chloride. NAD⁺ inhibits both Complex I-mediated and ammonium-stimulated H₂O₂ production. In the absence of stimulatory ammonium about half of the total NADH-supported hydrogen peroxide production is catalyzed by Complex I. In the presence of ammonium about 90% of the total hydrogen peroxide production is catalyzed by matrix located, ammonium-dependent enzyme(s).     

Why do bacteria use so many enzymes to scavenge hydrogen peroxide?

Hydrogen peroxide (H(2)O(2)) is continuously formed by the autoxidation of redox enzymes in aerobic cells, and it also enters from the environment, where it can be generated both by chemical processes and by the deliberate actions of competing organisms. Because H(2)O(2) is acutely toxic, bacteria elaborate scavenging enzymes to keep its intracellular concentration at nanomolar levels. Mutants that lack such enzymes grow poorly, suffer from high rates of mutagenesis, or even die. In order to understand how bacteria cope with oxidative stress, it is important to identify the key enzymes involved in H(2)O(2) degradation. Catalases and NADH peroxidase (Ahp) are primary scavengers in many bacteria, and their activities and physiological impacts have been unambiguously demonstrated through phenotypic analysis and through direct measurements of H(2)O(2) clearance in vivo. Yet a wide variety of additional enzymes have been proposed to serve similar roles: thiol peroxidase, bacterioferritin comigratory protein, glutathione peroxidase, cytochrome c peroxidase, and rubrerythrins. Each of these enzymes can degrade H(2)O(2) in vitro, but their contributions in vivo remain unclear. In this review we examine the genetic, genomic, regulatory, and biochemical evidence that each of these is a bonafide scavenger of H(2)O(2) in the cell. We also consider possible reasons that bacteria might require multiple enzymes to catalyze this process, including differences in substrate specificity, compartmentalization, cofactor requirements, kinetic optima, and enzyme stability. It is hoped that the resolution of these issues will lead to an understanding of stress resistance that is more accurate and perceptive.     

Why does viral RNA sometimes persist after recovery from acute infections?

DNA viruses often persist in the body of their host, becoming latent and recurring many months or years later. By contrast, most RNA viruses cause acute infections that are cleared from the host as they lack the mechanisms to persist. However, it is becoming clear that viral RNA can persist after clinical recovery and elimination of detectable infectious virus. This persistence can either be asymptomatic or associated with late progressive disease or nonspecific lingering symptoms, such as may be the case following infection with Ebola or Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Why does viral RNA sometimes persist after recovery from an acute infection? Where does the RNA come from? And what are the consequences?

Most RNA viruses cause acute infections that are cleared from the host as they lack the mechanisms to persist; however, phenomena such as "long COVID" suggest that viral RNA can persist after clinical recovery and elimination of detectable infectious virus. This Unsolved Mystery article explores the meaning, origins and consequences of such persistent RNA.     

Why does photosynthesis decrease with needle age in Pinus pinaster?

Rates of photosynthesis vary with foliage age and typically decline from full-leaf expansion until senescence occurs. This age-related decline in photosynthesis is especially important in species that retain foliage for several years, yet it is not known whether the internal conductance to CO₂ movement (g _i) plays any role. More generally, g _i has been measured in only a few conifers and has never been measured in leaves or needles older than 1 year. The effect of ageing on g _i was investigated in Pinus pinaster, a species that retains needle for 4 or more years. Measurements were made in autumn when trees were not water limited and after leaf expansion was complete. Rates of net photosynthesis decreased with needle age, from 8 μmol m⁻² s⁻¹ in fully expanded current-year needles to 4.4 μmol m⁻² s⁻¹ in 3-year-old needles. The relative limitation due to internal conductance (0.24–0.35 out of 1) was in all cases larger than that due to stomatal conductance (0.13–0.19 out of 1). Internal conductance and stomatal conductance approximately scaled with rates of photosynthesis. Hence, there was no difference among year-classes in the relative limitations posed by internal and stomatal conductance or evidence that they cause the age-related decline in photosynthesis. There was little evidence that the age-related decline in photosynthesis was due to decreases in contents of N or Rubisco. The decrease in rates of photosynthesis from current-year to older needles was instead related to a twofold decrease in rates of photosynthesis per unit nitrogen and V _cmax/Rubisco (i.e., in vivo specific activity).     

Why does intermittent hydrostatic pressure enhance the mineralization process in fetal cartilage?

The purpose of this study was to determine which factor is the most likely one to have stimulated the mineralization process in the in vitro experiments of Klein-Nulend et al. (Arth. Rheum., 29, 1002-1009, 1986), in which fetal cartilaginous metatarsals were externally loaded with an intermittent hydrostatic pressure, by compressing the gas phase above the culture medium. Analytical calculations excluded the possibility that the tissue was stimulated by changes in dissolved gas concentration, pH or temperature of the culture medium through compression of the gas phase. The organ culture experiments were also mechanically analyzed using a poroelastic finite element (FE) model of a partly mineralized metatarsal with compressible solid and fluid constituents. The results showed that distortional strains occurred in the region where mineralization proceeded. The value of this strain was, however, very sensitive to the value of the intrinsic compressibility modulus of the solid matrix (Ks). For realistic values of Ks the distortional strain was probably too small (about 2 microstrain) to have stimulated the mineralization. If the distortional strain was not the factor to have enhanced the mineralization process, then the only candidate variable left is the hydrostatic pressure itself. We hypothesize that the pressure may have created the physical environment enhancing the mineralization process. When hydrostatic pressure is applied, the balance of the chemical potential of water across cell membranes may be disturbed, and restored again by diffusion of ions until equilibrium is reached again. The diffusion of ions may have contributed to the mineralization process.     

A PDI-catalyzed thiol–disulfide switch regulates the production of hydrogen peroxide by human Ero1

Oxidative folding in the endoplasmic reticulum (ER) involves ER oxidoreductin 1 (Ero1)-mediated disulfide formation in protein disulfide isomerase (PDI). In this process, Ero1 consumes oxygen (O₂) and releases hydrogen peroxide (H₂O₂), but none of the published Ero1 crystal structures reveal any potential pathway for entry and exit of these reactants. We report that additional mutation of the Cys²⁰⁸–Cys²⁴¹ disulfide in hyperactive Ero1α (Ero1α-C104A/C131A) potentiates H₂O₂ production, ER oxidation, and cell toxicity. This disulfide clamps two helices that seal the flavin cofactor where O₂ is reduced to H₂O₂. Through its carboxyterminal active site, PDI unlocks this seal by forming a Cys²⁰⁸/Cys²⁴¹-dependent mixed-disulfide complex with Ero1α. The H₂O₂-detoxifying glutathione peroxidase 8 also binds to the Cys²⁰⁸/Cys²⁴¹ loop region. Supported by O₂ diffusion simulations, these data describe the first enzymatically controlled O₂ access into a flavoprotein active site, provide molecular-level understanding of Ero1α regulation and H₂O₂ production/detoxification, and establish the deleterious consequences of constitutive Ero1 activity.     

Caloric restriction and redox state: does this diet increase or decrease oxidant production?

Calorie restriction (CR) is well established to enhance the lifespan of a wide variety of organisms, although the mechanisms are still being uncovered. Recently, some authors have suggested that CR acts through hormesis, enhancing the production of reactive oxygen species (ROS), activating stress response pathways, and increasing lifespan. Here, we review the literature on the effects of CR and redox state. We find that there is no evidence in rodent models of CR that an increase in ROS production occurs. Furthermore, results in Caenorhabditis elegans and Saccharomyces cerevisiae suggesting that CR increases intracellular ROS are questionable, and probably cannot be resolved until adequate, artifact free, tools for real-time, quantitative, and selective measurements of intracellular ROS are developed. Overall, the largest body of work indicates that CR improves redox state, although it seems improbable that a global improvement in redox state is the mechanism through which CR enhances lifespan.     

How relevant is the reoxidation of ferrocytochrome c by hydrogen peroxide when determining superoxide anion production?

In a recent publication [(1987) FEBS Lett. 210, 195-198] the authors claim the use of cytochrome c to detect superoxide anion underestimates the real rate of superoxide anion formation on the basis that: (i) the rate of uric acid formation by xanthine oxidase is about 4-fold faster than the rate of cytochrome c reduction and (ii) hydrogen peroxide formed upon dismutation of the superoxide anion generated by xanthine oxidase is capable of reoxidizing ferrocytochrome c. That paper may have been misleading for readers not very familiar with the field of oxygen radicals, since both assumptions are, in fact, incorrect. In this report we demonstrate that the build up in concentration of H2O2 during most reactions in which superoxide anion is being produced is not enough to affect the rate of cytochrome c reduction. Our results suggest that the authors may have been misled by an artifact due to exposure of the samples containing H2O2 to UV light, which generates hydroxyl radicals by photolysis.     

Reactivity and endogenous modification by nitrite and hydrogen peroxide: does human neuroglobin act only as a scavenger?

NGB (human neuroglobin), a recently discovered haem protein of the globin family containing a six-co-ordinated haem, is expressed in nervous tissue, but the physiological function of NGB is currently unknown. As well as playing a role in neuronal O2 homoeostasis, NGB is thought to act as a scavenger of reactive species. In the present study, we report on the reactivity of metNGB (ferric-NGB), which accumulates in vivo as a result of the reaction of oxyNGB (oxygenated NGB) with NO, towards NO2- and H2O2. NO2- co-ordination of the haem group accounts for the activity of metNGB in the nitration of phenolic substrates. The two different metNGB forms, with and without the internal disulfide bond between Cys46 (seventh residue on the inter-helix region between helices C and D) and Cys55 (fifth residue on helix D), exhibit different reactivity, the former being more efficient in activating NO2-. The kinetics of the reactions, the NO2--binding studies and the analysis of the nitrated products from different substrates all support the hypothesis that metNGB is able to generate an active species with the chemical properties of peroxynitrite, at pathophysiological concentrations of NO2- and H2O2. Without external substrates, the targets of the reactive species generated by the metNGB/NO2-/H2O2 system are endogenous tyrosine (resulting in the production of 3-nitrotyrosine) and cysteine (oxidized to sulfinic acid and sulfonic acid) residues. These endogenous modifications were characterized by HPLC-MS/MS (tandem MS) analysis of metNGB after reaction with NO2- and H2O2 under various conditions. The internal S-S bond affects the functional properties of the protein. Therefore metNGB acts not only as scavenger of toxic species, but also as a target of the self-generated reactive species. Self-modification of the protein may be related to or inhibit its postulated neuroprotective activity.     

Why does experimental insulin deficiency lead to a decrease in removal of very low density-triglyceride from plasma?

We have previously suggested that mechanisms other than reduced lipoprotein lipase (LPL) activity might contribute to the defect in plasma removal of very low density lipoprotein (VLDL)-triglyceride (TG) observed in insulin-deficient rats. To further evaluate this phenomenon, removal rates of TG in nonfractionated plasma, as well as in isolated lipoprotein fractions obtained from insulin-deficient and control rats, were compared in a new, sensitive in vivo bioassay system (estradiol-treated male rats with a consistently low endogenous VLDL-TG pool). Removal of TG in nonfractionated plasma from insulin-deficient rats was slower than that of control rats: 3.0 +/- 0.3 vs 1.6 +/- 0.2 min (P less than 0.001). No difference was found in removal rate of isolated VLDL-TG (2.5 +/- 0.3 vs 2.6 +/- 0.4 min), or in removal rates of TG carried in other lipoprotein fractions. We next determined the effect of injection into normal rats of aliquots of dialyzed lipoprotein-free (D greater than 1.215) plasma from insulin-deficient and control rats on the removal rate of normal VLDL-TG, and found that lipoprotein-free plasma from insulin-deficient rats significantly (P less than 0.01) prolonged removal of normal VLDL-TG (4.3 +/- 0.4 to 6.8 +/- 0.7 min). This same fraction did not interfere with the in vitro hydrolysis of normal VLDL-TG by post-heparin LPL. Thus, a factor in the D greater than 1.215 plasma fraction of insulin-deficient rats is present which interferes with the rate of removal of TG from plasma, unrelated to inhibition of LPL activity.     

Why does the bud-galling sawfly,Euura mucronata,attack long shoots?

Summary The bud-galling sawfly, Euura mucronata, attacked longer shoot length classes on its host, Salix cinerea, more frequently than shorter shoots. Shoot length accounted for 76 to 93 percent of the variance in number of galls per 100 shoots in three habitats: forest, watermeadow, and lakeside. The reasons for this pattern were addressed with studies on shoot length in relation to: 1. Number of resources (buds) per shoot; 2. Success in establishment of larvae in galls; 3. Gall size and resources per gall; and 4. Survival of larvae after establishment as influenced by plant resistance and natural enemy attack. The most important factors proved to be success in establishment of larvae, with percent of variance accounted for ranging from 57 to 77 percent in three of four sites where relationships were significant, and survival after establishment of larvae, with variance accounted for ranging from 40 to 54 percent in the same three sites. The pattern of survival was dictated by plant resistance and not by natural enemies. These two additive factors resulted in a general relationship across all sites of increasing emergence of fully developed larvae per cohort as shoot length increased, accounting for 78 percent of the variance. These adaptive advantages to attacking longer shoots are sufficient to account for the pattern of increased probability of shoots being attacked as they increase in length.     

Why,when and how does the poly(A) tail shorten during mRNA translation?

• 1.1. The length of the poly(A) tail at the 3'-end of mRNA may control protein synthesis by bringing the 3'-end in close proximity to the 5'-end of the noncoding region as well as increasing the duration of mRNA translation by its binding to the poly(A) binding protein.
• 2.2. The rate-limiting step in the decay of the body of the message is the shortening of a long poly(A) tail during mRNA translation. The shortening of the poly(A) tail occurs during pre-elongation in the protein synthesis cycle.
• 3.3. The shortening of the poly(A) tail during mRNA translation may not involve RNase activity, however poly(A) binding protein seems to play a role, at least in part, in shortening of the poly(A) tail.

     

Why are we shaped differently, and why does it matter?

Body fat distribution is an important predictor of metabolic abnormalities in obese humans. Dysregulation of free fatty acid (FFA) release, especially from upper body subcutaneous adipose tissue, appears to contribute substantially to these metabolic disturbances. Why different individuals preferentially store fat in upper vs. lower body subcutaneous fat or subcutaneous vs. visceral fat is not completely understood. Current evidence suggests that defects in regional lipolysis are not the cause of net fat retention in larger fat depots. Regional variations in the storage of fatty acids, both meal derived and direct reuptake, and storage of circulating FFAs that may help to explain why some depots expand at the expense of others have been reported. We review the quantitative data on regional lipolysis, meal, and FFA storage in adults to provide an overview of fat balance differences in adults with different fat distribution patterns.     

Why is uncompetitive inhibition so rare?: A possible explanation,with implications for the design of drugs and pesticides

Uncompetitive inhibition is much less common in nature than consideration of enzyme structure and mechanism might lead one to expect. A possible explanation may be that uncompetitive inhibition of an enzyme in a metabolic pathway can have enormously larger effects on the concentrations of metabolic intermediates than competitive inhibition, under circumstances where their effects on the kinetics of the isolated enzyme are very similar. The severely toxic effects that an uncompetitive inhibitor might be expected to have may have caused enzymes to have evolved in such a way that there has been selection against structures that might favour uncompetitive inhibition.     

Why does some pollen lack apertures? A review of inaperturate pollen in eudicots

Apertures are key characters of pollen grains with systematic importance in angiosperms. They function as sites for pollen tube exit, water uptake, transfer of recognition substances and accommodation of volume changes. Not all pollen has apertures; inaperturate pollen (lacking obvious apertures) characterizes many angiosperm groups, especially in early divergent angiosperms and monocots, but also eudicots. In order to expand our knowledge of the systematic distribution, possible functional significance and development of inaperturate pollen in angiosperms, this review focuses on inaperturate and cryptoaperturate (with hidden apertures) pollen in the large eudicot clade, which comprises about 75% of present‐day angiosperm species. It includes new TEM observations of inaperturate pollen from four exemplar taxa selected from different parts of the eudicot phylogeny. Two categories of inaperturate (including cryptoaperturate) pollen occur in eudicots. (1) Sterile attractant or feeding pollen associated with functional dioecy has evolved iteratively at least six times in conjunction with complex breeding systems in the core eudicots. (2) Fertile pollen has evolved numerous times independently throughout eudicots, though generally in a relatively small number of individual taxa. Notable exceptions are the petaliferous crotonoid Euphorbiaceae s.s., in which fertile inaperturate pollen occurs in c. 1500 species, and two subfamilies of Apocynaceae s.l. (Secamonoideae and Asclepiadoideae) with c. 2500 species with fertile inaperturate pollen in pollinia. Fertile inaperturate pollen is sometimes (but not always) associated with an aquatic habit, parasitism, insectivory, heterostyly, anemophily or pollinia. Most fertile inaperturate pollen has a thin exine, or the exine is largely restricted to isolated components (muri, protuberances, subunits) separated by thinner areas which probably function as apertures. In cryptoaperturate pollen, the aperture is covered by continuous exine which probably has a protective function, similar to an operculum. Developmentally, inaperturate pollen is not associated with any particular tetrad type or meiotic spindle orientation (unlike some apertures) due to the absence of a colpal shield of endoplasmic reticulum or other organelles and hence is independent of microsporogenesis type. The lack of a colpal shield during the tetrad stage of development permits complete deposition of first primexine and then exine around each microspore, possibly mediated by the action of the DEX1 protein. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155 , 29–48.     

Why does Coomassie Brilliant Blue R interact differently with different proteins? A partial answer

Dimethyl sulfoxide was found to be effective for extraction of Coomassie Brilliant Blue R-250 (Coomassie R) from stained proteins on polyacrylamide gel slices. A good correlation was found between the ability of different proteins to bind Coomassie R and their capacity for interaction with Coomassie Brilliant Blue G-250 (Coomassie G) in solution. Scatchard analysis showed that the number of Coomassie R ligands bound to each protein molecule is approximately proportional to the number of positive charges on the protein, about 1.5-3 dye molecules/charge.