SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline.

Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X-ray footprinting of biomolecules performed for the first time at the X-ray Metrology beamline at the SOLEIL synchrotron radiation source. The installation at this beamline of a stopped-flow apparatus for sample delivery, an irradiation capillary and an automatic sample collector enabled the X-ray footprinting study of the structure of the soluble protein factor H (FH) from the human complement system as well as of the lipid-associated hydrophobic protein S3 oleosin from plant seed. Mass spectrometry analysis showed that the structural integrity of both proteins was not affected by the short exposition to the oxygen radicals produced during the irradiation. Irradiated molecules were subsequently analysed using high-resolution mass spectrometry to identify and locate oxidized amino acids. Moreover, the analyses of FH in its free state and in complex with complement C3b protein have allowed us to create a map of reactive solvent-exposed residues on the surface of FH and to observe the changes in oxidation of FH residues upon C3b binding. Studies of the solvent accessibility of the S3 oleosin show that X-ray footprinting offers also a unique approach to studying the structure of proteins embedded within membranes or lipid bodies. All the biomolecular applications reported herein demonstrate that the Metrology beamline at SOLEIL can be successfully used for synchrotron X-ray footprinting of biomolecules.

Systematic resequencing of X-chromosome synaptic genes in autism spectrum disorder and schizophrenia.

Autism spectrum disorder (ASD) and schizophrenia (SCZ) are two common neurodevelopmental syndromes that result from the combined effects of environmental and genetic factors. We set out to test the hypothesis that rare variants in many different genes, including de novo variants, could predispose to these conditions in a fraction of cases. In addition, for both disorders, males are either more significantly or more severely affected than females, which may be explained in part by X-linked genetic factors. Therefore, we directly sequenced 111 X-linked synaptic genes in individuals with ASD (n = 142; 122 males and 20 females) or SCZ (n = 143; 95 males and 48 females). We identified >200 non-synonymous variants, with an excess of rare damaging variants, which suggest the presence of disease-causing mutations. Truncating mutations in genes encoding the calcium-related protein IL1RAPL1 (already described in Piton et al. Hum Mol Genet 2008) and the monoamine degradation enzyme monoamine oxidase B were found in ASD and SCZ, respectively. Moreover, several promising non-synonymous rare variants were identified in genes encoding proteins involved in regulation of neurite outgrowth and other various synaptic functions (MECP2, TM4SF2/TSPAN7, PPP1R3F, PSMD10, MCF2, SLITRK2, GPRASP2, and OPHN1).

[Usefulness of biomarkers of sepsis in the ICU]. / Utilité des biomarqueurs du sepsis en réanimation.

Despite some progress, the mortality of severe sepsis and septic shock remains high. Immunotherapy directed against inflammatory mediators failed, but new treatments more specifically tailored to individual situations are actively investigated. C-reactive protein (CRP) and procalcitonin (PCT) have not demonstrated to be useful for individual prognostic stratification. New biomarkers such as pancreatic stone protein (PSP) or growth arrest specific protein 6 (Gas6) could improve this prediction. Combined with the clinical course, "PCT" allows to tailor individually the duration of antibiotic therapy in ICU patients. This still contested innovative approach significantly reduces overall exposure to antibiotics.

At5g50600 encodes a member of the short-chain dehydrogenase reductase superfamily with 11beta- and 17beta-hydroxysteroid dehydrogenase activities associated with Arabidopsis thaliana seed oil bodies.

In a previous work, we presented evidence for the presence of a protein encoded by At5g50600 in oil bodies (OBs) from Arabidopsis thaliana [P. Jolivet, E. Roux, S. D'Andrea, M. Davanture, L. Negroni, M. Zivy, T. Chardot, Protein composition of oil bodies in Arabidopsis thaliana ecotype WS, Plant Physiol. Biochem. 42 (2004) 501-509]. Using specific antibodies and proteomic techniques, we presently confirm the existence of this protein, which is a member of the short-chain steroid dehydrogenase reductase superfamily. We have measured its activity toward various steroids (cholesterol, dehydroepiandrosterone, cortisol, corticosterone, estradiol, estrone) and NAD(P)(H), either within purified OBs or as a purified bacterially expressed chimera. Both enzymatic systems (OBs purified from A. thaliana seeds as well as the chimeric enzyme) exhibited hydroxysteroid dehydrogenase (HSD) activity toward estradiol (17beta-hydroxysteroid) with NAD+ or NADP+, NADP+ being the preferred cofactor. Low levels of activity were observed with cortisol or corticosterone (11beta-hydroxysteroids), but neither cholesterol nor DHEA (3beta-hydroxysteroids) were substrates, whatever the cofactor used. Similar activity profiles were found for both enzyme sources. Purified OBs were found to be also able to catalyze estrone reduction (17beta-ketosteroid reductase activity) with NADPH. The enzyme occurring in A. thaliana OBs can be classified as a NADP+-dependent 11beta-,17beta-hydroxysteroid dehydrogenase/17beta-ketosteroid reductase. This enzyme probably corresponds to AtHSD1, which is encoded by At5g50600. However, its physiological role and substrates still remain to be determined.

Protein components of low-density lipoproteins purified from hen egg yolk.

To identify apoproteins present in purified low-density lipoproteins from hen egg yolk in relation with their emulsifying properties, they have been separated by SDS-PAGE. We identified two different proteins by liquid chromatography-tandem mass spectrometry analysis of the peptides obtained by the trypsin digestion of protein gel bands. Apovitellenin I was identified as a monomer and a dimer. Its amino acid sequence was totally confirmed, and molecular mass determination by liquid chromatography-mass spectrometry showed that it did not present post-translational modifications but only a slight heterogeneity by the loss of one or two amino acids at the C-terminal part of the protein. Apolipoprotein B was identified into seven bands corresponding to fragments resulting of a processing of the hen blood apo-B protein. The identity of the fragments was determined by the observation of the sequence coverage by trypsin peptides and the sequence alignment with homologous human blood apolipoprotein B-100.

Characterization of an exocellular protein phosphatase with dual substrate specificity from the yeast Yarrowia lipolytica.

In previous work, the major endocellular protein phosphatase activity has been identified in the secretory yeast Yarrowia lipolytica as a PP2A. The aim of the present work was to seek the presence of one protein phosphatase excreted in the exocellular medium and to study its activity during yeast growth in media supplemented or not supplemented with inorganic phosphate. Protein phosphatase was purified and activity was assayed by following the dephosphorylation of three substrates, [32P]casein, phosphotyrosine and a synthetic tyrosine-phosphorylated peptide. Phosphatase activity recovered in the medium after 25 h culture was greatly enhanced by Pi-deficiency. After several purification steps, the enzyme preparation presents an apparent electrophoretic homogeneity on SDS-PAGE with associated phosphoseryl/threonyl and phosphotyrosyl activities. The kinetic properties exclude contamination by a copurified protein and it is concluded that the two activities are carried by the same single proteic species. It was characterized by gel filtration as a 33 kDa protein with one single subunit demonstrated by SDS-PAGE. An absolute requirement for reducing-agents is observed suggesting that the enzyme contains at least one essential reactive cysteinyl residue. Optimum pH value is 6.1, apparent K(m) for phosphotyrosine was calculated to be 760 microM and Hill coefficient 3.2 indicating a rather high cooperativity. These results showed that the involvement of alkaline and/or acid phosphatase was unlikely. In conclusion, a protein phosphatase distinct from endocellular PP2A is secreted by Yarrowia lipolytica and characterized as a phosphotyrosine protein phosphatase with associated phosphoseryl/threonyl activity.

[Predictive microbiology. Toward an operational tool to help our appraisal]. / Microbiologie prévisionnelle. Pour un outil opérationnel d'aide à l'expertise.

Knowledge of microbiological behavior in foods is a prerequisite to food processing quality control. From the mid eighties to the mid nineties, much research established growth and secondary models adapted to the main food pathogens, taking into consideration ecology factors such as temperature, pH, and Nacl concentration. This work led to the development of software to predict micro-organism growth. These devices were found however to be of little use because growth in limit conditions was poorly estimated and food composition or structure were not considered. More factors have to be taken into account when building a useful and informative tool for diagnosis. Food data and impact of food processing must be considered.

Towards a humanized PPARγ reporter system for in vivo screening of obesogens.

Overeating and lack of exercise are major contributors to the current obesity epidemic, but environmental contaminants, or obesogens, are also considered to be potential actors. A common obesogen target is the Peroxisome Proliferator Activated Receptor Gamma (PPARγ). Screening for exogenous obesogens requires in vivo systems as many xenobiotics exert their effects through metabolites. We thus developed a humanized in vivo PPARγ reporter model, using Xenopus laevis larvae, a species possessing metabolic capacities comparable to mammals. A somatic transgenesis approach was used to co-express an expression vector for the human PPARγ protein simultaneously with one of a series of reporter vectors, each containing a PPARγ Response Element (PPRE)-eGFP sequence. Treatment of tadpoles with PPARγ agonists, antagonists or candidate obesogens, significantly modulated eGFP expression. Thus, the system provides a promising proof of principle for a sensitive and reliable humanized in vivo tool to screen both novel PPARγ drug ligands and potential endocrine disruptors or obesogens targeting this receptor.

[Gregarines from South Korea (author's transl)]. / Grégarines de la Corée du sud

Study of 14 species of Gregarines from terrestrial arthropods (Myriapoda and Insecta) of south Korea. Some of them (Ramicephalus ozakii, Gregarina monoducta, Hoplorhynchus ozakii, Stylocephalus bahli) are typically asiatic whereas the others were already described from identical or similar european hosts.

Determination of glycolic acid level in higher plants during photorespiration by stable isotope dilution mass spectrometry with double-labeling experiments.

Determination of glycolic acid by stable isotope dilution was applied to the measurement of the glycolic acid pool size in tomato and maize leaves during photorespiration. Detached leaves were maintained in the presence of 18O2; [13C]glycolate was added to the foliar extract as an internal standard and the mixture of biological glycolate and [13C]glycolate was analyzed by combined gas chromatography-mass spectrometry. The level of foliar glycolate pool was measured via the 13C label, and 18O incorporation was determined.

Characterization of major protein phosphatases from selected species of Kluyveromyces. Comparison with protein phosphatases from Yarrowia lipolytica.

Casein phosphatase activities have been identified in five yeast strains grown on Pi-deficient medium. Maximal endocellular activities appeared in the exponential phase. Exocellular phosphatases were significantly produced from Yarrowia lipolytica W-29 and Kluyveromyces marxianus, in the early stationary phase. Major phosphatases from K. marxianus were one heavy acid phosphatase composed of 64-67 kDa subunits, which could be secreted in the medium, and one type 2A protein phosphatase with an apparent molecular mass of 147 kDa and a 52 kDa catalytic subunit dissociated by 80% ethanol treatment. The characteristics of phosphatases purified from K. marxianus were compared with those previously purified from Y. lipolytica.

A protein kinase is located in the micellar fraction of fresh pasteurized skimmed farm milk.

Recombinant protein kinase CK2 from the yeast Schizosaccharomyces pombe is able to phosphorylate casein in skimmed pasteurized milk. We could incorporate up to 540 pmol of phosphate into 50 microg milk proteins, i.e., 0.26 P/mol caseins. To better understand the action of protein kinase CK2 on milk proteins, we have compared the action of rspCK2alpha on milk, and on different casein micellar subfractions isolated from milk by ultracentrifugation. In contrast to the situation observed with phosphocaseinate, alpha(s) casein was the best substrate for rspCK2alpha, whether milk or micellar fractions were used as substrates. We have characterized the protein content of different micellar fractions obtained by ultracentrifugation of cow milk using capillary zone electrophoresis. We confirm that the kappa casein content of micelles largely decreases when their size increases. In contrast, the alpha(s) casein content slightly increased with micelles size and beta casein content remained constant. All of the micellar fractions were substrates for rspCK2alpha, but a significant amount of intrinsic protein kinase activity was also found. The intrinsic protein kinase used added ATP as phosphate donor, and was only slightly sensitive to high heparin concentration. It could phosphorylate micellar casein in milk ultrafiltrate, in the absence of addition of any metallic cofactor. Its activity was only slightly affected by the addition of either MgCl2 or MnCl2. CaCl2 activated the enzyme significantly. The intrinsic kinase lost its activity with time, and could incorporate from 9 to 26% of the total phosphate incorporated in the presence of rspCK2a. Alpha(s) casein was the best substrate of the intrinsic kinase, followed by beta casein. In the presence of CaCl2, the intrinsic kinase was found to incorporate up to 470 pmol of phosphate into 50 microg of milk proteins.

Purification and characterization of a type 2A protein phosphatase from Yarrowia lipolytica grown on a phosphate-deficient medium.

Intracellular protein phosphatase activity has been identified in the yeast Yarrowia lipolytica. This activity was maximal early in its exponential growth phase, and it was enhanced by Pi-deficiency of the culture medium. On a Pi-deficient medium, the major protein phosphatase was purified. This enzyme was dissociated with 80% ethanol treatment, its activity was slightly increased (30%) with heparine and largely enhanced (1.5 to 3-fold) with polycations. This enzyme could be classified as a type 2A protein phosphatase. It is composed of a catalytic subunit and other subunits. Its optimum pH value is 7.2, the apparent Km for casein is 37 microM and the apparent velocity 3.6 pmol hydrolyzed32 Pi min-1 pmol-1 enzyme.

Time-co-ordinated control of glycogen synthase, protein phosphatase 2A and protein kinase CK2 during culture growth in Yarrowia lipolytica in relation to glycogen metabolism.

In the growth course of the lipolytic yeast Yarrowia lipolytica, the activities of protein phosphatase 2A (PP2A) and glycogen synthase (GS) rise during the exponential phase and concomitantly glycogen storage occurs in the cells. There is also an increase in the independence ratio (RI) indicating a shift from an inactive phosphorylated GS form to an active dephosphorylated GS form. During the early stationary phase, an increase in protein kinase CK2 (CK2) activity, a reversion of RI variation and a glycogen content decrease are observed. GS activity proved to be a good indicator of early culture growth phase. Experiments carried out with enzymes purified from Y. lipolytica show strong RI variations upon the action of CK2 and PP2Ac, and 32P incorporation into GS protein through phosphorylation by CK2. GS activity would be controlled by the sequential action of PP2A and CK2.