Protonless 13C direct detection NMR: characterization of the 37 kDa trimeric protein CutA1

The major limitation of nuclear magnetic resonance spectroscopy arises from the increase of nuclear transverse relaxation rates with increasing molecular mass. This causes reduction in spectral resolution and coherence transfer efficiency. The use of 2H-labeling to eliminate 1H-mediated relaxation pathways and the constructive use of cross correlation effects (TROSY, CRINEPT) alleviate the phenomenon. An alternative approach is to use direct detection of heteronuclei. Specifically designed 13C direct detection experiments can complement the set of 1H-based NMR experiments commonly used for structure determination providing an additional source of information less affected by the detrimental transverse relaxation effect. We applied this novel methodology to the study of the CutA1 protein (12.3 kDa) from E. coli that forms a homotrimer in solution with a total molecular mass of 37 kDa. In this work we demonstrate that the information available from 13C direct detection experiments makes it possible to completely assign the NMR resonances of the backbone of this 37 kDa trimeric protein without the need of deuteration. The structural and dynamical knowledge obtained for this system may contribute to understand its biological role.     

Occurrence of copper proteins through the three domains of life: a bioinformatic approach

In high-throughput genome-level protein investigation efforts, such as Structural Genomics, the systematic experimental characterization of metal-binding properties (i.e., the investigation of the metalloproteome) is not always pursued and remains far from trivial. In the present work, we have applied a bioinformatic approach to investigate the occurrence of (putative) copper-binding proteins in 57 different organisms spanning the entire tree of life. We found that the size of the copper proteome is generally less than 1% of the total proteome of an organism, in both eukaryotes and prokaryotes. The occurrence of copper-binding proteins is relatively scarce when compared to that of zinc-binding proteins and of non-heme iron proteins. This may be due to both poorer bioavailability (in particular with respect to iron in the ancient world) and the complexity of copper chemistry and the risks associated with it, which may have adversely affected natural selection of copper-binding proteins. The present analysis shows that there is a strong relationship between the metal coordination sphere and protein function. A network involving proteins having roles in both copper transport and respiration was identified, parts or all of which are detected in the majority of the organisms examined.     

A decade of irrigation transforms the soil microbiome of a semi‐arid pine forest

The impact of climate change on the soil microbiome potentially alters the biogeochemical cycle of terrestrial ecosystems. In semi‐arid environments, water availability is a major constraint on biogeochemical cycles due to the combination of high summer temperatures and low rainfall. Here, we explored how 10 years of irrigation of a water‐limited pine forest in the central European Alps altered the soil microbiome and associated ecosystem functioning. A decade of irrigation stimulated tree growth, resulting in higher crown cover, larger yearly increments of tree biomass, increased litter fall and greater root biomass. Greater amounts of plant‐derived inputs associated with increased primary production in the irrigated forest stands stimulated soil microbial activity coupled with pronounced shifts in the microbiome from largely oligotrophic to more copiotrophic lifestyles. Microbial groups benefitting from increased resource availabilities (litter, rhizodeposits) thrived under irrigation, leading to enhanced soil organic matter mineralization and carbon respired from irrigated soils. This unique long‐term study provides new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a water‐limited pine forest ecosystem and improves our understanding of the persistency of long‐term soil carbon stocks in a changing climate.     

Differential Effects of Angiotensin II and Eledoisin on Monoamine Oxidase A and B Activities in Rat Brain

Intracerebroventricular injections of angiotensin II caused 108, 62, and 54% increases in monoamine oxidase A activities in rat hippocampus, hypothalamus, and striatum, respectively. These activatory effects were abolished by simultaneous injections of eledoisin. No significant changes of monoamine oxidase B activities were found under the same experimental conditions. Neither angiotensin II nor elodoisin changed substrate/inhibitor affinities of both isoenzymes. These data indicate that angiotensin II and tachykinin transmitter systems may exert opposite, long-term regulatory effects on monoaminergic neurons in rat brain.     

1H-NMR and relaxometry of copper-containing dimers in proteins

Summary The water-proton nuclear-magnetic-relaxation dispersion profiles have been analyzed for Cu₂Zn₂-superoxide dismutase (SOD) and Cu₂-alkaline phosphatase (AP). The electronic relaxation times are derived, together with structural information. The effect of magnetic coupling with another copper ion in Cu₂Cu₂SOD and Cu₂Cu₂AP is discussed. It is shown that the electronic relaxation times of copper(II) essentially do not change. The opposite happens with Cu₂Co₂SOD, Cu₂Co₂AP and Cu₂Ni₂SOD in which fast-relaxing metal ions provide relaxation mechanisms for copper(II) as well. In these cases the systems can be studied through high-resolution NMR spectroscopy.     

Ectomycorrhizas: their role in forest ecosystems under the impact of acidifying pollutants

The physiologically active lateral rootlets of all main trees in temperate forests are colonised by ectomycorrhizal fungi, forming so-called ectomycorrhizas. These symbiotic organs are the sites of exchange of nutrients, mainly P and N, provided from the fungal partner, and C from the host. Emerging from the ectomycorrhizas, fungal hyphae exploit the soil for the mobilisation and absorption of water and nutrient elements. By doing so, they connect the tree roots intimately with the soil and provide anchorage. The deposition of acidifying pollutants into forest ecosystems is a potential threat to the health and vitality of forest trees because it leads to the acidification and eutrophication of forest soils. Pollutants are also a threat to the functioning of ectomycorrhizas. Increased N concentrations in the soil lead to enhanced fungal N uptake and storage, and to enhanced N transfer to the host plants, and therefore to higher plant biomass of above ground parts. In consequence, there is a decrease of C allocation to the plant roots. This in turn leads to reduced ectomycorrhization, and to reduced production of external mycelia and fruiting bodies. Soil acidification leads to enhanced availability of Al, heavy metals, and radionuclides in the soil, all of which can be toxic to plants and fungi. Reduced growth of roots and hyphae are amongst the first symptoms. In ectomycorrhizas, the hyphae of the fungal tissues contain vacuolar polyphosphates which have the ability to bind Al, heavy metals, radionuclides and N. These electronegative polymers of phosphates represent an effective storage and detoxifying mechanism which otherwise is lacking in roots. Therefore, ectomycorrhizas have the potential to increase the tolerance of trees to acidifying pollutants and to the increased availability in the soil of toxic elements.     

Reduced expression of frataxin extends the lifespan of Caenorhabditis elegans

Defects in the expression of the mitochondrial protein frataxin cause Friedreich's ataxia, an hereditary neurodegenerative syndrome characterized by progressive ataxia and associated with reduced life expectancy in humans. Homozygous inactivation of the frataxin gene results in embryonic lethality in mice, suggesting that frataxin is required for organismic survival. Intriguingly, the inactivation of many mitochondrial genes in the nematode Caenorhabditis elegans by RNAi extends lifespan. We therefore investigated whether inactivation of frataxin by RNAi-mediated suppression of the frataxin homolog gene (frh-1) would also prolong lifespan in the nematode. Frataxin-deficient animals have a small body size, reduced fertility and altered responses to oxidative stress. Importantly, frataxin suppression by RNAi significantly extends lifespan in C. elegans.     

Furostanol saponins and quercetin glycosides from the leaves of Helleborus viridis L

Phytochemical analysis of the polar extracts of the leaves of Helleborus viridis (Ranunculaceae) resulted in the isolation of two new furostanol saponins (25R)-26-[(alpha-L-rhamnopyranosyl)oxy]-22alpha-methoxyfurost-5-en-3beta-yl O-beta-D-glucopyranosyl-(1-->3)-O-[6-acetyl-beta-D-glucopyranosyl-(1-->3)]-O-beta-D-glucopyranoside (1) and (25R)-26-[(alpha-L-rhamnopyranosyl)oxy]-22alpha-methoxyfurost-5-en-3beta-yl O-beta-D-glucopyranosyl-(1-->3)-O-beta-D-glucopyranosyl-(1-->3)-O-beta-D-glucopyranoside (2) and three new quercetin glycosides, quercetin 3-O-(2-E-caffeoyl)-alpha-L-arabinopyranosyl-(1-->2)-beta-D-galactopyranoside-7-O-beta-d-glucopyranoside (3), quercetin 3-O-(2-E-caffeoyl)-alpha-L-arabinopyranosyl-(1-->2)-beta-D-galactopyranoside (4), and quercetin 3-O-alpha-L-arabinopyranosyl-(1-->2)-beta-D-galactopyranoside (5). The structures of the new compounds were determined by spectroscopic analysis, including 2D NMR data and mass spectrometry.