Quaternary structure change as a mechanism for the regulation of thymidine kinase 1-like enzymes

The human cytosolic thymidine kinase (TK) and structurally related TKs in prokaryotes play a crucial role in the synthesis and regulation of the cellular thymidine triphosphate pool. We report the crystal structures of the TK homotetramer from Thermotoga maritima in four different states: its apo-form, a binary complex with thymidine, as well as the ternary structures with the two substrates (thymidine/AppNHp) and the reaction products (TMP/ADP). In combination with fluorescence spectroscopy and mutagenesis experiments, our results demonstrate that ATP binding is linked to a substantial reorganization of the enzyme quaternary structure, leading to a transition from a closed, inactive conformation to an open, catalytic state. We hypothesize that these structural changes are relevant to enzyme function in situ as part of the catalytic cycle and serve an important role in regulating enzyme activity by amplifying the effects of feedback inhibitor binding.     

Get the most out of your metagenome: computational analysis of environmental sequence data

New advances in sequencing technologies bring random shotgun sequencing of ecosystems within reach of smaller labs, but the complexity of metagenomics data can be overwhelming. Recently, many novel computational tools have been developed to unravel ecosystem properties starting from fragmented sequences. In addition, the so-called 'comparative metagenomics' approaches have allowed the discovery of specific genomic and community adaptations to environmental factors. However, many of the parameters extracted from these data to describe the environment at hand (e.g. genomic features, functional complement, phylogenetic composition) are interdependent and influenced by technical aspects of sample preparation and data treatment, leading to various pitfalls during analysis. To avoid this and complement existing initiatives in data standards, we propose a minimal standard for metagenomics data analysis ('MINIMESS') to be able to take full advantage of the power of comparative metagenomics in understanding microbial life on earth.     

Development of an assay for the intermembrane transfer of cholesterol by Niemann-Pick C2 protein

Niemann-Pick type C disease is an inherited fatal disorder characterized by the accumulation of unesterified cholesterol and other lipids in the endosomal/lysosomal compartment. Two independent genes responsible for this neurodegenerative disorder have been identified, but the precise functions of the encoded Niemann-Pick C1 (NPC1) and C2 (NPC2) proteins are not yet known. We developed a cell-free assay for measuring intermembrane lipid transport and examined the ability of bovine NPC2 (bNPC2) for intermembrane cholesterol transfer. NPC2 specifically extracts cholesterol from phospholipid bilayers and catalyzes intermembrane transfer to acceptor vesicles in a dose- and time-dependent manner. This transfer activity is dependent on temperature, pH, ionic strength, lipid composition of the model membranes, and the ratio of donor to acceptor vesicles. In model membranes, the presence of the lysosomal anionic phospholipids bis(monooleoylglycero)phosphate and phosphatidyl inositol significantly stimulated cholesterol transfer by NPC2, whereas bis(monomyristoylglycero)phosphate, phosphatidyl serine, and phosphatidic acid had no effect. Moreover, ceramide stimulated cholesterol transfer slightly, whereas sphingomyelin reduced cholesterol transfer rates. With our assay system we identified for the first time the ability of other lysosomal proteins, most notably the GM2-activator protein, to mediate intermembrane cholesterol transfer. This assay system promises to be a valuable tool for further quantitative and mechanistic studies of protein-mediated lipid transfer.     

A novel Dps-type protein from insect gut bacteria catalyses hydrolysis and synthesis of N-acyl amino acids

A novel type of a microbial N-acyl amino acid hydrolase (AAH) from insect gut bacteria was purified, cloned and functionally characterized. The enzyme was obtained from Microbacterium arborescens SE14 isolated from the foregut of larvae of the generalist herbivore Spodoptera exigua. The substrates of AAH are N-acyl-glutamines previously reported to elicit plant defence reactions after introduction into the leaf during feeding. The isolated AAH catalyses the hydrolysis of the amide bond (K(m) = 36 micromol l(-1)) and, less efficient, the formation (K(m) = 3 mmol l(-1)) of the elicitor active N-acyl amino acids. The AAH from M. arborescens SE14 shows no homology to known fatty acyl amidases (EC 3.5.1.4) but belongs to the family of Dps proteins (DNA-binding protein from starved cell). In line with other DPS proteins AAH is a homododecamer (monomer 17 181 Da) and contains iron atoms (c. 1-16 iron atoms per subunit). Unlike genuine DPS proteins the enzyme does not significantly bind DNA. Amino acid hydrolase is the first member of the DPS family that catalyses the cleavage or formation of amide bonds. The participation of a microbial enzyme in the homeostasis of N-acyl-glutamines in the insect gut adds further complexity to the interaction between plants and their herbivores.     

TRPM6 and TRPM7--Gatekeepers of human magnesium metabolism

Human magnesium homeostasis primarily depends on the balance between intestinal absorption and renal excretion. Magnesium transport processes in both organ systems - next to passive paracellular magnesium flux - involve active transcellular magnesium transport consisting of an apical uptake into the epithelial cell and a basolateral extrusion into the interstitium. Whereas the mechanism of basolateral magnesium extrusion remains unknown, recent molecular genetic studies in patients with hereditary hypomagnesemia helped gain insight into the molecular nature of apical magnesium entry into intestinal brush border and renal tubular epithelial cells. Patients with Hypomagnesemia with Secondary Hypocalcemia (HSH), a primary defect in intestinal magnesium absorption, were found to carry mutations in TRPM6, a member of the melastatin-related subfamily of transient receptor potential (TRP) ion channels. Before, a close homologue of TRPM6, TRPM7, had been characterized as a magnesium and calcium permeable ion channel vital for cellular magnesium homeostasis. Both proteins share the unique feature of an ion channel fused to a kinase domain with homology to the family of atypical alpha kinases. The aim of this review is to summarize the data emerging from clinical and molecular genetic studies as well as from electrophysiologic and biochemical studies on these fascinating two new proteins and their role in human magnesium metabolism.     

Analysis of the potential for a comprehensive approach towards LCA and EMS in Japan

Sustainable development can only be achieved if industry adoptsboth product related and organisation related environmental management tools, such as Life Cycle Assessment (LCA) and Environmental Management Systems (EMS). In Japan, EMS (ISO 14001) is more widely applied than LCA (ISO 14040). Therefore,one means by which Japanese industries could be motivated to adopt and use LCA is to relate LCA-activities to the policies and instruments of ISO 14001. The potential of such a comprehensive approach was analysed by a survey of 270 Japanese enterprises (response rate 45%). The results indicate that 19% of the responding representatives had responsibilities for both LCA and EMS, while the remaining only work in one of both fields. A statement in the company’s/ plant’s Environmental Policy of ISO 14001, stating that LCA is to be used as part of the EMS, was found in 42% of all companies. A surprising number (39%) either already use, or plan to use, LCA and EMS as combinated/integrated tools. A strong argument for the establishment of a comprehensive approach can be seen in the perception of the usefulness of LCA, which was rated significantly higher in companies that acknowledged the complementary potential of LCA and EMS.     

The Hydrophobic Core Sequence Modulates the Neurotoxic and Secondary Structure Properties of the Prion Peptide 106-126

The neurodegeneration seen in spongiform encephalopathies is believed to be mediated by protease-resistant forms of the prion protein (PrP). A peptide encompassing residues 106-126 of human PrP has been shown to be neurotoxic in vitro. The neurotoxicity of PrP106-126 appears to be dependent upon its adoption of an aggregated fibril structure. To examine the role of the hydrophobic core, AGAAAAGA, on PrP106-126 toxicity, we performed structure-activity analyses by substituting two or more hydrophobic residues for the hydrophilic serine residue to decrease its hydrophobicity. A peptide with a deleted alanine was also synthesized. We found all the peptides except the deletion mutant were no longer toxic on mouse cerebellar neuronal cultures. Circular dichroism analysis showed that the nontoxic PrP peptides had a marked decrease in beta-sheet structure. In addition, the mutants had alterations in aggregability as measured by turbidity, Congo red binding, and fibril staining using electron microscopy. These data show that the hydrophobic core sequence is important for PrP106-126 toxicity probably by influencing its assembly into a neurotoxic structure. The hydrophobic sequence may similarly affect aggregation and toxicity observed in prion diseases.     

Affinity Purification of Proteoglycans that Bind to the Amyloid Protein Precursor of Alzheimer's Disease

Abstract: The binding of the amyloid protein precursor (APP) to heparan sulfate proteoglycans has been shown to stimulate the neurite-promoting activity of APP. In this study, proteoglycans that bind with high affinity to APP were characterized. Conditioned medium from cultures of postnatal day 3 mouse brain cells was applied to an affinity column containing a peptide homologous to a heparin-binding domain of APP. A fraction 17-fold enriched in proteoglycans was recovered by elution with a salt gradient. APP bound saturably and with high affinity to the affinity-purified proteoglycan fraction. Scatchard analysis of the binding showed that APP bound to high- and low-affinity sites with equilibrium dissociation constants of 1.4 × 10⁻¹¹ and 6.5 × 10⁻¹⁰ M , respectively. APP, in conjunction with the affinity-purified proteoglycan fraction, promoted neurite outgrowth. The affinity-purified proteoglycan fraction contained a heparan sulfate proteoglycan and a chondroitin sulfate proteoglycan. Digestion of the affinity-purified fraction with heparitinase I revealed a core protein of 63–69-kDa molecular mass, whereas digestion with chondroitinase ABC revealed a core protein of 100–110 kDa. The results suggest that expression of specific APP-binding proteoglycans may be an important step in the regulation of the neurite outgrowth-promoting activity of APP.     

Physiological acclimation to drought stress in Solidago canadensis

Solidago canadensis is an invasive species from North America that is spreading across Europe, Australia and temperate Asia. We hypothesized that the species' wide ecological amplitude is also based on its potential in hydraulic acclimation, and analyzed hydraulic and anatomical properties along a transect with decreasing soil humidity. Stem hydraulic conductivity, vulnerability to drought‐induced embolism, stomatal closure during dehydration and xylem‐anatomical parameters were quantified at three sites. At the humid site, specific hydraulic conductivity of stems (1.0 ± 0.2 kg m^–1 MPa^–1 s^–1) was about twofold higher, and leaf‐specific conductivity about 1.5 times higher (3.1 ± 0.5 kg m^–1 MPa^–1 s^–1) than at the dry site. Water potential (Ψ) at 50% loss of conductivity was ?3.7 ± 0.1 MPa at the dry site and ?3.1 ± 0.2 MPa at the humid site (September). Vulnerability to drought‐induced embolism decreased along the transect and over the vegetation period. At drier sites, stomata started closing at lower Ψ while complete stomatal closure was reached at less negative Ψ (12% of maximum stomatal conductance: –2.5 ± 0.0 and ?3.0 ± 0.2 MPa at the dry and humid site). The safety margin between stomatal closure and 50% loss of conductivity was 1.2 and 0.2 MPa at the dry and humid sites. The observed variability indicated an efficient acclimation in hydraulic conductivity and safety: plants at dry sites exhibited lower specific hydraulic conductivity, higher embolism resistance and broader safety margins, signifying a trade‐off between the hydraulic safety and efficiency. The observed intraspecific plasticity in hydraulic and anatomical traits may help to explain the invasive potential of this species.