Nitrotyrosine and protein carbonyls are equally distributed in HT22 cells after nitrosative stress

The generation of reactive oxygen and nitrogen species is an inevitable result of cellular metabolism and environmental influence. Such oxidation processes are always combined with the formation of various protein oxidation products. Environmental oxidants might either be activated inside the cell or act by themselves. Therefore, differences in the localization of oxidant formation might change the major compartment of oxidant action. Therefore, we employed NO donors (SNOC, DETA/NO, and Spe/NO) alone or in combination with the redox-cycling bipyridinium compound paraquat, the superoxide- and NO-releasing compound SIN-1, the relatively more lipophilic oxidants tert-butyl and cumene hydroperoxide, and peroxynitrite itself to test the ability of these compounds to generate oxidized and nitrated proteins in various cellular compartments. Combined treatment with oxidants and nitrating compounds led to the formation of protein carbonyls and nitrotyrosine with a severalfold higher concentration in the cytosol, compared to the nucleus. In fluorescence microscopy studies, the resulting protein modifications show a similar distribution of oxidized proteins and nitrotyrosine with highest concentrations in the perinuclear area. Studying the time- and concentration-dependent formation and degradation of protein carbonyls and nitrated proteins large similarities could be measured. Therefore, it can be concluded that formation, localization, and kinetics of protein carbonyl and nitrotyrosine formation parallel each other depending on the stress-inducing agent.     

From selection to complementarity: shifts in the causes of biodiversity-productivity relationships in a long-term biodiversity experiment

In a 10-year (1996-2005) biodiversity experiment, the mechanisms underlying the increasingly positive effect of biodiversity on plant biomass production shifted from sampling to complementarity over time. The effect of diversity on plant biomass was associated primarily with the accumulation of higher total plant nitrogen pools (N g m-2) and secondarily with more efficient N use at higher diversity. The accumulation of N in living plant biomass was significantly increased by the presence of legumes, C4 grasses, and their combined presence. Thus, these results provide clear evidence for the increasing effects of complementarity through time and suggest a mechanism whereby diversity increases complementarity through the increased input and retention of N, a commonly limiting nutrient.     

Resource use patterns predict long-term outcomes of plant competition for nutrients and light

An 11-year competition experiment among combinations of six prairie perennial plant species showed that resource competition theory generally predicted the long-term outcome of competition. We grew each species in replicated monocultures to determine its requirements for soil nitrate (R*) and light (I*). In six pairwise combinations, the species with the lower R* and I* excluded its competitor, as predicted by theory. In the remaining two pairwise combinations, one species had a lower R*, and the second had a lower I*; these species pairs coexisted, although it is unclear whether resource competition alone was responsible for their coexistence. Smaller differences in R* or I* between competing species led to slower rates of competitive exclusion, and the influence of R* differences on the rate of competitive exclusion was more pronounced on low-nitrogen soils, while the influence of I* differences was more pronounced on high-nitrogen (low-light) soils. These results were not explained by differences in initial species abundances or neutrality. However, only a few of our paired species coexisted under our experimentally imposed conditions (homogeneous soils, high seeding densities, minimal disturbance, regular water, and low herbivory levels), suggesting that other coexistence mechanisms help generate the diversity observed in natural communities.     

Tree diversity in relation to maximum tree height: evidence for the harshness hypothesis of species diversity gradients

Marks et al. (Ecology Letters, 19, 2016, 743) showed tree species richness correlates with maximum tree height, and interpret this as evidence that the environmental stressors that limit tree height also act as ecological filters on species richness. Here, we strengthen these arguments by further addressing the roles of environmental covariates and beta diversity.     

Chaperones, but not oxidized proteins, are ubiquitinated after oxidative stress

After oxidative stress, proteins that are oxidatively modified are degraded by the 20S proteasome. However, several studies have documented an enhanced ubiquitination of yet unknown proteins. Because ubiquitination is a prerequisite for degradation by the 26S proteasome in an ATP-dependent manner this raises the question whether these proteins are also oxidized and, if not, what proteins need to be ubiquitinated and degraded after oxidative conditions. By determination of oxidized and ubiquitinated proteins we demonstrate here that most oxidized proteins are not preferentially ubiquitinated. However, we were able to confirm an increase in ubiquitinated proteins 16 h after oxidative stress. Therefore, we isolated ubiquitinated proteins from hydrogen peroxide-treated cells, as well as from control cells and cells treated with lactacystin, an irreversible proteasome inhibitor, and identified some of these proteins by MALDI tandem mass spectrometry. As a result we obtained 24 different proteins that can be categorized into the following groups: chaperones, energy metabolism, cytoskeleton/intermediate filaments, and protein translation/ribosome biogenesis. The special set of identified, ubiquitinated proteins confirms the thesis that ubiquitination upon oxidative stress is not a random process to degrade the mass of oxidized proteins, but concerns a special group of functional proteins.     

Plant diversity drives soil microbial biomass carbon in grasslands irrespective of global environmental change factors

Soil microbial biomass is a key determinant of carbon dynamics in the soil. Several studies have shown that soil microbial biomass significantly increases with plant species diversity, but it remains unclear whether plant species diversity can also stabilize soil microbial biomass in a changing environment. This question is particularly relevant as many global environmental change (GEC) factors, such as drought and nutrient enrichment, have been shown to reduce soil microbial biomass. Experiments with orthogonal manipulations of plant diversity and GEC factors can provide insights whether plant diversity can attenuate such detrimental effects on soil microbial biomass. Here, we present the analysis of 12 different studies with 14 unique orthogonal plant diversity × GEC manipulations in grasslands, where plant diversity and at least one GEC factor (elevated CO₂, nutrient enrichment, drought, earthworm presence, or warming) were manipulated. Our results show that higher plant diversity significantly enhances soil microbial biomass with the strongest effects in long‐term field experiments. In contrast, GEC factors had inconsistent effects with only drought having a significant negative effect. Importantly, we report consistent non‐significant effects for all 14 interactions between plant diversity and GEC factors, which indicates a limited potential of plant diversity to attenuate the effects of GEC factors on soil microbial biomass. We highlight that plant diversity is a major determinant of soil microbial biomass in experimental grasslands that can influence soil carbon dynamics irrespective of GEC.     

Disruption of ClC-3, a chloride channel expressed on synaptic vesicles, leads to a loss of the hippocampus

Several plasma membrane chloride channels are well characterized, but much less is known about the molecular identity and function of intracellular Cl- channels. ClC-3 is thought to mediate swelling-activated plasma membrane currents, but we now show that this broadly expressed chloride channel is present in endosomal compartments and synaptic vesicles of neurons. While swelling-activated currents are unchanged in mice with disrupted ClC-3, acidification of synaptic vesicles is impaired and there is severe postnatal degeneration of the retina and the hippocampus. Electrophysiological analysis of juvenile hippocampal slices revealed no major functional abnormalities despite slightly increased amplitudes of miniature excitatory postsynaptic currents. Mice almost lacking the hippocampus survive and show several behavioral abnormalities but are still able to acquire motor skills.     

Metabolism of 4-hydroxy-2-nonenal in human polymorphonuclear leukocytes

Intracellular metabolism of 4-hydroxy-2-nonenal (HNE), a major product and mediator of oxidative stress and inflammation, is analyzed in resting and fMLP-stimulated human polymorphonuclear leukocytes (PMNL), where this compound is generated during activation of the respiratory burst. HNE consumption rate in PMNL is very low, if compared to other cell types (rat hepatocytes, rabbit fibroblasts), where HNE metabolism is always an important part of secondary antioxidative defense mechanisms. More than 98% of HNE metabolites are identified. The pattern of HNE intermediates is quite similar in stimulated and resting PMNL - except for higher water formation in resting PMNL - while the initial velocity of HNE degradation is somewhat higher in resting cells, 0.44 instead of 0.28 nmol/(min × 10⁶ cells). The main products of HNE metabolism are 4-hydroxynonenoic acid (HNA), 1,4-dihydroxynonene (DHN) and the glutathione adducts with HNE, HNA, and DHN. Protein-bound HNE and water account for about 3-4% of the total HNE derivatives in stimulated cells, while in resting cells protein-bound HNE and water are 4% and 20%, respectively. Cysteinyl-glycine-HNE adduct and mercapturic acids contribute to about 5%.     

HIV-1 Nef Binds a Subpopulation of MHC-I throughout Its Trafficking Itinerary and Down-regulates MHC-I by Perturbing Both Anterograde and Retrograde Trafficking

The HIV protein Nef is thought to mediate immune evasion and promote viral persistence in part by down-regulating major histocompatibility complex class I protein (MHC-I or HLA-I) from the cell surface. Two different models have been proposed to explain this phenomenon as follows: 1) stimulation of MHC-I retrograde trafficking from and aberrant recycling to the plasma membrane, and 2) inhibition of anterograde trafficking of newly synthesized HLA-I from the endoplasmic reticulum to the plasma membrane. We show here that Nef simultaneously uses both mechanisms to down-regulate HLA-I in peripheral blood mononuclear cells or HeLa cells. Consistent with this, we found by using fluorescence correlation spectroscopy that a third of diffusing HLA-I at the endoplasmic reticulum, Golgi/trans-Golgi network, and the plasma membrane (PM) was associated with Nef. The binding of Nef was similarly avid for native HLA-I and recombinant HLA-I A2 at the PM. Nef binding to HLA-I at the PM was sensitive to specific inhibition of endocytosis. It was also attenuated by cyclodextrin disruption of PM lipid micro-domain architecture, a change that also retarded lateral diffusion and induced large clusters of HLA-I. In all, our data support a model for Nef down-regulation of HLA-I that involves both major trafficking itineraries and persistent protein-protein interactions throughout the cell.