Sequential backbone assignment of uniformly 13C-labeled RNAs by a two-dimensional P(CC)H-TOCSY triple resonance NMR experiment

Summary A new ¹H−¹³C−³¹P triple resonance experiment is described which allows unambigous sequential backbone assignment in ¹³C-labeled oligonucleotides via through-bond coherence transfer from ³¹P via ¹³C to ¹H. The approach employs INEPT to transfer coherence from ³¹P to ¹³C and homonuclear TOCSY to transfer the ¹³C coherence through the ribose ring, followed by ¹³C to ¹H J-cross-polarisation. The efficiencies of the various possible transfer pathways are discussed. The most efficient route involves transfer of ³¹P_i coherence via C4′_i and C4′_i-1, because of the relatively large J′_PC4 couplings involved. Via the homonuclear and heteronuclear mixing periods, the C4′_i and C4′_i-1 coherences are subsequently transferred to, amongst others, H1′_i and H1′_i-1, respectively, leading to a 2D ¹H−³¹P spectrum which allows a sequential assignment in the ³¹P−¹H1′ region of the spectrum, i.e. in the region where the proton resonances overlap least. The experiment is demonstrated on a ¹³C-labeled RNA hairpin with the sequence 5′(GGGC-CAAA-GCCU)3′.     

Disturbance does not have a significant impact on waders in an estuary close to conurbations: importance of overlap between birds and people in time and space

Disturbance of wildlife is a potential cause of conservation concern, not least to overwintering waders Charadrii inhabiting estuaries close to conurbations where human recreational and economic activities are often concentrated. Disturbance from people on and alongside intertidal foraging areas could make it more difficult for birds to survive until spring in good condition by reducing the time available for foraging, increasing energy requirements and displacing birds to poorer foraging areas. We adopted a two-part approach to testing whether such significant impacts occurred in a Special Protection Area where disturbance risk was high because of its small size and close proximity to conurbations. In part one, we recorded over the whole estuary during stages of the tidal cycle when part or all of the intertidal zone was exposed and so accessible to waders (i.e. on receding, low and advancing tides): (1) the numbers and activities of people on the intertidal flats and on the adjacent land in those places where people were visible to waders in the intertidal zone and (2) the numbers of waders present and disturbed into flight, the flight distance and flight duration in the ‘overlap’ areas where people did disturb waders. People occurred on < 25% of the 938 ha of intertidal flats, but most waders foraged on mudflats, whereas most people were on sandflats. People on land were visible to foraging waders along < 35% of the 16.5 km of shoreline. Waders and people were therefore substantially separated in space. Within overlap areas, people and waders were often frequently separated in time: for example, people on land mostly disturbed waders when only the upper shore levels were exposed. The average overwintering wader spent < 0.1% of its foraging time during daylight flying away from people and the additional energy expenditure was equivalent to < 0.02% of its daily requirements. The comparison made in part two between our study area and two comparable estuaries showed that the number of visits each day to the overlap areas would need to be 29 or 43 times greater for disturbance to have lowered the birds’ body condition and winter survival. Both parts of the study therefore suggested strongly that the amount of disturbance was too trivial to have a significant impact on waders. It is concluded that: (1) to properly assess disturbance risk to waders, both extensive and intensive observations must be made on the behaviour of people and birds to quantify the extent to which they overlap in space and time, and (2) it should not be assumed that an estuary's close proximity to conurbations, and the presence of large numbers of people in the vicinity of the SPA, necessarily implies a significant disturbance risk to waders.     

Metabolomics of dietary Fatty Acid restriction in patients with phenylketonuria

Background

Patients with phenylketonuria (PKU) have to follow a lifelong phenylalanine restricted diet. This type of diet markedly reduces the intake of saturated and unsaturated fatty acids especially long chain polyunsaturated fatty acids (LC-PUFA). Long-chain saturated fatty acids are substrates of mitochondrial fatty acid oxidation for acetyl-CoA production. LC-PUFA are discussed to affect inflammatory and haemostaseological processes in health and disease. The influence of the long term PKU diet on fatty acid metabolism with a special focus on platelet eicosanoid metabolism has been investigated in the study presented here.

Methodology/Principal Findings

12 children with PKU under good metabolic control and 8 healthy controls were included. Activated fatty acids (acylcarnitines C6–C18) in dried blood and the cholesterol metabolism in serum were analyzed by liquid chromatographic tandem mass spectrometry (LC-MS/MS). Fatty acid composition of plasma glycerophospholipids was determined by gas chromatography. LC-PUFA metabolites were analyzed in supernatants by LC-MS/MS before and after platelet activation and aggregation using a standardized protocol. Patients with PKU had significantly lower free carnitine and lower activated fatty acids in dried blood compared to controls. Phytosterols as marker of cholesterol (re-) absorption were not influenced by the dietary fatty acid restriction. Fatty acid composition in glycerophospholipids was comparable to that of healthy controls. However, patients with PKU showed significantly increased concentrations of y-linolenic acid (C18:3n-6) a precursor of arachidonic acid. In the PKU patients significantly higher platelet counts were observed. After activation with collagen platelet aggregation and thromboxane B₂ and thromboxane B₃ release did not differ from that of healthy controls.

Conclusion/Significance

Long-term dietary fatty acid restriction influenced the intermediates of mitochondrial beta-oxidation. No functional influence on unsaturated fatty acid metabolism and platelet aggregation in patients with PKU was detected.     

Site-specific photocrosslinking to probe interactions of Arf1 with proteins involved in budding of COPI vesicles

ADP-ribosylation factor 1 (Arf1) plays an important role in early and intra-Golgi protein trafficking. During this process, Arf1 interacts with many different proteins and other molecules that regulate its state of activation or are involved in its intracellular function. To determine which of these proteins interact directly with Arf1 during coat protein type I (COPI) vesicle biogenesis, we probed the molecular environment of Arf1 by use of site-specific photocrosslinking. This method was first used successfully in the field of protein trafficking to study the mechanisms involved in protein translocation across the endoplasmic reticulum during protein synthesis. In such a hydrophobic environment, crosslink yields of up to 30% have been observed. We have now applied this method to study the mechanism of vesicle budding from the cytosolic face of the Golgi apparatus, an aqueous environment. Although the crosslink yield is significantly lower under these conditions, due to predominant reaction of the photolabile probes with water, a specific interaction of Arf1 with subunits of coatomer, the major coat protein of COPI vesicles, could readily be identified.     

A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly

Proteins modified by multiubiquitin chains are the preferred substrates of the proteasome. Ubiquitination involves a ubiquitin-activating enzyme, E1, a ubiquitin-conjugating enzyme, E2, and often a substrate-specific ubiquitin-protein ligase, E3. Here we show that efficient multiubiquitination needed for proteasomal targeting of a model substrate requires an additional conjugation factor, named E4. This protein, previously known as UFD2 in yeast, binds to the ubiquitin moieties of preformed conjugates and catalyzes ubiquitin chain assembly in conjunction with E1, E2, and E3. Intriguingly, E4 defines a novel protein family that includes two human members and the regulatory protein NOSA from Dictyostelium required for fruiting body development. In yeast, E4 activity is linked to cell survival under stress conditions, indicating that eukaryotes utilize E4-dependent proteolysis pathways for multiple cellular functions.     

ArfGAP1 Activity and COPI Vesicle Biogenesis

Golgi-derived coat protein I (COPI) vesicles mediate transport in the early secretory pathway. The minimal machinery required for COPI vesicle formation from Golgi membranes in vitro consists of (i) the hetero-heptameric protein complex coatomer, (ii) the small guanosine triphosphatase ADP-ribosylation factor 1 (Arf1) and (iii) transmembrane proteins that function as coat receptors, such as p24 proteins. Various and opposing reports exist on a role of ArfGAP1 in COPI vesicle biogenesis. In this study, we show that, in contrast to data in the literature, ArfGAP1 is not required for COPI vesicle formation. To investigate roles of ArfGAP1 in vesicle formation, we titrated the enzyme into a defined reconstitution assay to form and purify COPI vesicles. We find that catalytic amounts of Arf1GAP1 significantly reduce the yield of purified COPI vesicles and that Arf1 rather than ArfGAP1 constitutes a stoichiometric component of the COPI coat. Combining the controversial reports with the results presented in this study, we suggest a novel role for ArfGAP1 in membrane trafficking.     

High energy phosphate transfer by NDPK B/Gβγcomplexes - an alternative signaling pathway involved in the regulation of basal cAMP production

The activation of heterotrimeric G proteins induced by G protein coupled receptors (GPCR) is generally believed to occur by a GDP/GTP exchange at the G protein α -subunit. Nevertheless, nucleoside diphosphate kinase (NDPK) and the β-subunit of G proteins (Gβ) participate in G protein activation by phosphate transfer reactions leading to the formation of GTP from GDP. Recent work elucidated the role of these reactions. Apparently, the NDPK isoform B (NDPK B) forms a complex with β; γ; dimers in which NDPK B acts as a histidine kinase phosphorylating G#x03B2; at His266. Out of this high energetic phosphoamidate bond the phosphate can be transferred specifically onto GDP. The formed GTP binds to the G protein α -subunit and thus activates the respective G protein. Evidence is presented, that this process occurs independent of the classical GPCR-induced GTP/GTP exchange und thus contributes, e.g. to the regulation of basal cAMP synthesis in cells.     

The karyotype and ultrastructural characteristics of spontaneous preimplantation mouse parthenotes

Karyotypic and light and electron microscopical analyses were made of spontaneous preimplantation mouse parthenotes from the LT/Sv inbred strain. It was found that the activated oocyte and developing embryos were diploid. We believe that diploidization is achieved by the oogonium undergoing a premeiotic mitosis without cytokinesis followed by two meiotic divisions, thus producing diploid parthenotes. The developmental events with respect to membrane specialization, such as junctional complexes, were similar to those observed in fertilized embryos. A unique feature of the developing parthenote was the failure of the mitochondria to change during the morula stage. The mitochondria retained a few irregularly oriented cristae rather than many transversely oriented ones observed in morulae developing from fertilized eggs. The significance of this observation is discussed.     

Sequence of the halobacterial glycosaminoglycan

The cell-surface glycoprotein of halobacterium contains a sulfated repeating unit saccharide chain, similar to the mammalian glycosaminoglycans. The composition of a presumptive repeating pentasaccharide unit of this glycosaminoglycan is 1 GlcNAc, 1 GalNAc, 1 Gal, 1 GalA (where GalA represents galacturonic acid), 1 3-O-methyl-GalA, and 2 SO42-. Linkage to protein of this glycoconjugate involves the hitherto unique unit Asn-GalNAc, with the N-linked asparagine residue being the second NH2-terminal amino acid and part of the common N-linked glycosyl acceptor sequence Asn-X-Thr(Ser). Transfer of the completed, sulfated glycosaminoglycan from its lipid precursor to the protein occurs at the cell surface, and the presence of this sulfated saccharide chain in the cell-surface glycoprotein seems to be required to maintain the structural integrity of the rod-shaped halobacteria. In this paper, we report the complete saccharide structure of this N-linked glycosaminoglycan. This structure is deduced from chemical analyses of fragments that were isolated after hydrazinolysis and subsequent nitrous acid deamination or after mild acidic hydrolysis of purified Pronase-derived glycosaminoglycan-peptides. The halobacterial glycosaminoglycan consists, on the average, of 10 repeating pentasaccharide units of the following structure. (formula: see text) The reducing end N-acetylgalactosamine residue is linked directly to the asparagine, without a special saccharide linker region.     

Phenotypic Profiling of Scedosporium aurantiacum,an Opportunistic Pathogen Colonizing Human Lungs

Genotyping studies of Australian Scedosporium isolates have revealed the strong prevalence of a recently described species: Scedosporium aurantiacum. In addition to occurring in the environment, this fungus is also known to colonise the respiratory tracts of cystic fibrosis (CF) patients. A high throughput Phenotype Microarray (PM) analysis using 94 assorted substrates (sugars, amino acids, hexose-acids and carboxylic acids) was carried out for four isolates exhibiting different levels of virulence, determined using a Galleria mellonella infection model. A significant difference was observed in the substrate utilisation patterns of strains displaying differential virulence. For example, certain sugars such as sucrose (saccharose) were utilised only by low virulence strains whereas some sugar derivatives such as D-turanose promoted respiration only in the more virulent strains. Strains with a higher level of virulence also displayed flexibility and metabolic adaptability at two different temperature conditions tested (28 and 37°C). Phenotype microarray data were integrated with the whole-genome sequence data of S. aurantiacum to reconstruct a pathway map for the metabolism of selected substrates to further elucidate differences between the strains.