Characterization of greater middle eastern genetic variation for enhanced disease gene discovery

The Greater Middle East (GME) has been a central hub of human migration and population admixture. The tradition of consanguinity, variably practiced in the Persian Gulf region, North Africa, and Central Asia1-3, has resulted in an elevated burden of recessive disease4. Here we generated a whole-exome GME variome from 1,111 unrelated subjects. We detected substantial diversity and admixture in continental and subregional populations, corresponding to several ancient founder populations with little evidence of bottlenecks. Measured consanguinity rates were an order of magnitude above those in other sampled populations, and the GME population exhibited an increased burden of runs of homozygosity (ROHs) but showed no evidence for reduced burden of deleterious variation due to classically theorized ‘genetic purging’. Applying this database to unsolved recessive conditions in the GME population reduced the number of potential disease-causing variants by four- to sevenfold. These results show variegated genetic architecture in GME populations and support future human genetic discoveries in Mendelian and population genetics

Implication du diacyglycérol pyrophosphate et des lipides phosphate phosphatases dans la signalisation de l'acide abscissique chez Arabidopsis thaliana

L acide abscissique (ABA) est une phytohormone impliquée dans de nombreux processus de développement des plantes. L ABA s accumule également en réponse à des stress abiotiques et participe à l établissement de la résistance à ces stress par la régulation de l expression de gènes et des mouvements stomatiques. La signalisation cellulaire de l ABA est très complexe et fait intervenir de nombreux partenaires protéiques et messagers secondaires. En particulier, le rôle des phospholipides a été démontré sur des cellules en suspension d A. thaliana. En effet, la forme phosphorylée de l acide phosphatidique (PA), le diacylglycérol pyrophosphate (DGPP), s accumule de façon transitoire en réponse à l ABA et mime les effets de l ABA sur l induction de l expression du gène RAB18. Mon travail de thèse apporte des éléments renforçant l hypothèse d un rôle de messager secondaire du DGPP dans la voie de signalisation de l ABA. Des analyses transcriptomiques ont montré que le DGPP contrôle l expression de nombreux gènes régulés par l ABA. De plus, le DGPP mime les effets de l ABA en induisant l entrée de Ca2+ dans les cellules et en régulant l activité de canaux anioniques membranaires. L utilisation d inhibiteurs de canaux calciques et anioniques nous a permis de proposer une séquence d évènements précoces de la signalisation de l ABA, nécessaires au contrôle de l expression de gènes, impliquant le Ca2+, le DGPP et les courants anioniques. Afin de préciser le rôle du PA et du DGPP dans la signalisation de l ABA, l étude d enzymes du catabolisme du PA et du DGPP, les Lipide Phosphate Phosphatases (LPP), a été entreprise. Les LPP déphosphorylent le DGPP en PA et le PA en diacylglycérol (DAG). Quatre gènes codent des LPP dans le génome d A. thaliana, AtLPP1, 2, 3 et 4. Des mutants d insertion homozygotes ont été obtenus pour les gènes AtLPP1,2 et 3, et leurs réponses à l ABA ont été étudiées au cours de tests physiologiques. Seul le mutant knock-out Atlpp2-2 présente un phénotype différent de celui du sauvage lors de l inhibition de la germination, l induction artificielle de la sénescence foliaire et l induction de la fermeture stomatique par l ABA. En outre, les teneurs en PA et DGPP d Atlpp2-2 sont plus élevées que celles du sauvage. De plus, des études transcriptomiques ont révélé que la régulation de l expression génique par l ABA est perturbée chez Atlpp2-2. Tous ces résultats suggèrent que la protéine AtLPP2 est impliquée dans la signalisation de l ABA, probablement en régulant les pools des deux messagers secondaires, DGPP et PA.PARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Analysis of the effect of heat shock on wheat storage protein

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Proteomic analysis of the effect of heat stress on hexaploid wheat grain: Characterization of heat-responsive proteins from non-prolamins fraction

43 ref.The effect of heat stress on hexaploid wheat grain proteome was recently analyzed in our previous works. Proteomic tools allowed the characterization of heat-responsive proteins of total endosperm, composed mainly of prolamins. The present work completes this study; our aim was to analyze the effect of heat stress on the water-soluble fraction, composed essentially of albumins and globulins. These proteins were separated by two-dimensional electrophoresis (2-DE), visualized by Coomassie Brilliant Blue (CBB) staining and analyzed by Melanie-3 software. Of the 43 heat-changed proteins, 24 were found to be up-regulated whereas 19 spot proteins were down-regulated. All of these proteins were subjected to matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) followed by database searching which allowed the identification of 42 spots. Of these, some were enzymes involved in different metabolic pathways of plants, such as granule-bound starch synthase and glucose-1-phosphate adenyltransferase, involved in the starch synthesis pathway; beta-amylase, involved in carbohydrate metabolism, and the ATP synthase beta-chain that was related to four heat-decreased proteins. Moreover, five heat up-regulated proteins showed similarities with small heat shock proteins while three other spots were related to elongation factors or eucaryotic translation initiation factors. Proteins involved in abiotic stresses or in plant defense mechanism were also identified and are discussed

Protein Tyrosine Kinases and Protein Tyrosine Phosphatases Are Involved in Abscisic Acid-Dependent Processes in Arabidopsis Seeds and Suspension Cells.

International audienc

Induction of Abscisic Acid-Regulated Gene Expression by Diacylglycerol Pyrophosphate Involves Ca(2+) and Anion Currents in Arabidopsis Suspension Cells

Diacylglycerol pyrophosphate (DGPP) was recently shown to be a possible intermediate in abscisic acid (ABA) signaling. In this study, reverse transcription-PCR of ABA up-regulated genes was used to evaluate the ability of DGPP to trigger gene expression in Arabidopsis (Arabidopsis thaliana) suspension cells. At5g06760, LTI30, RD29A, and RAB18 were stimulated by ABA and also specifically expressed in DGPP-treated cells. Use of the Ca(2+) channel blockers fluspirilene and pimozide and the Ca(2+) chelator EGTA showed that Ca(2+) was required for ABA induction of DGPP formation. In addition, Ca(2+) participated in DGPP induction of gene expression via stimulation of anion currents. Hence, a sequence of Ca(2+), DGPP, and anion currents, constituting a core of early ABA-signaling events necessary for gene expression, is proposed

Diacylglycerol kinases activate tobacco NADPH oxidase-dependent oxidative burst in response to cryptogein

SPE IPM UB INRA SUPDATInternational audienceCryptogein is a 10 kDa-protein secreted by the oomycete Phytophthora cryptogea that activates defence mechanisms in tobacco plants. Among early signalling events triggered by this microbial-associated molecular pattern is a transient apoplastic oxidative burst which is dependent on the NADPH oxidase activity of the RESPIRATORY BURST OXIDASE HOMOLOG (RBOH) isoform D. Using radioactive [33P]-orthophosphate labelling of tobacco Bright Yellow-2 suspension cells, we here provide in vivo evidence for a rapid accumulation of phosphatidic acid (PA) in response to cryptogein due to the coordinated onset of phosphoinositide-dependent phospholipase C and diacylglycerol kinase (DGK) activities. Both enzyme specific inhibitors and silencing of the phylogenetic cluster III of the tobacco DGK family were found to reduce PA production upon elicitation and to strongly decrease the RBOHD-mediated oxidative burst. Therefore, it appears that PA originating from DGK controls NADPH-oxidase activity. Amongst cluster III DGKs, the expression of DGK5-like was up-regulated in response to cryptogein. Besides DGK5-like is likely to be the main cluster III DGK isoform silenced in one of our mutant line, making it a strong candidate for the observed response to cryptogein. The relevance of these results is discussed with regard to early signalling lipid-mediated events in plant immunity