Fine tuning of signaling pathways is essential for cells to cope with sudden environmental variations. This delicate balance is maintained in particular by protein kinases that control the activity ...of target proteins by reversible phosphorylation. In addition to homologous eukaryotic enzymes, bacteria have evolved some specific Ser/Thr/Tyr protein kinases without any structural resemblance to their eukaryotic counterparts. Here, we show that a previously identified family of ATPases, broadly conserved among bacteria, is in fact a new family of protein kinases with a Ser/Thr/Tyr kinase activity. A prototypic member of this family, YdiB from Bacillus subtilis, is able to autophosphorylate and to phosphorylate a surrogate substrate, the myelin basic protein. Two crystal structures of YdiB were solved (1.8 and 2.0Å) that display a unique ATP-binding fold unrelated to known protein kinases, although a conserved HxD motif is reminiscent of that found in Hanks-type protein kinases. The effect of mutations of conserved residues further highlights the unique nature of this new protein kinase family that we name ubiquitous bacterial kinase. We investigated the cellular role of YdiB and showed that a ∆ydiB mutant was more sensitive to paraquat treatment than the wild type, with ~13% of cells with an aberrant morphology. In addition, YdiE, which is known to participate with both YdiC and YdiB in an essential chemical modification of some specific tRNAs, is phosphorylated in vitro by YdiB. These results expand the boundaries of the bacterial kinome and support the involvement of YdiB in protein translation and resistance to oxidative stress in B. subtilis.
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•A new widely conserved protein kinase family has been identified in bacteria.•The YdiB/YjeE family is an S/T/Y protein kinase family.•3D structure of YdiB shows a unique ATP-binding fold.•YdiB is involved in the control of oxidative stress.•YdiB phosphorylates YdiE and might control protein translation.
La matrice extracellulaire est un réseau tridimensionnel complexe qui joue le rôle de support aux cellules ainsi que de réservoir de molécules bioactives régulant le comportement cellulaire. Elle est ...composée de 1027 protéines chez l’Homme (Naba et al., Matrix Biol. 2016), 274 protéines constituant le matrisome et 753 associées (facteurs de croissance et protéines régulatrices de la matrice extracellulaire) et de 6 glycosaminoglycanes dont 5 sulfatés. La matrice extracellulaire est impliquée dans de nombreuses pathologies (Bonnans et al., Nat. Rev. Mol. Cell Biol. 2014). La lysyl oxydase, responsable de la réticulation des collagènes et de l’élastine est impliquée dans de nombreux cancers. La matrice extracellulaire est un réservoir de fragments bioactifs, nommés matricryptines, qui sont libérés par protéolyse des biomolécules de la matrice et régulent de nombreux processus biologiques tels que l’angiogenèse et l’adipogenèse (Ricard-Blum et Vallet Matrix Biol. 2017). Nous avons exprimé en cellules humaines plusieurs matricryptines dont les ectodomaines des collagènes membranaires XIII, XVII, XXIII et XXV et identifié leurs partenaires extracellulaires. Nous avons caractérisé le propeptide de la lysyl oxydase par SEC-MALS, diffusion dynamique de la lumière et par SAXS et avons modélisé à partir des données de SAXS sa structure tridimensionnelle. Nous avons identifié 17 nouveaux partenaires de ce fragment et analysé le mutant Arg158Gln dépourvu d’activité biologique. Cette mutation identifiée chez l’Homme inhibe les activités anti-prolifératives du propeptide et est associée à un risque accru de cancer du sein (Min et al., Cancer Res. 2009). Nous avons exprimé la lysyl oxydase mature et modélisé sa structure tridimensionnelle en utilisant toutes les données disponibles. Les interactions identifiées au cours de ce travail ont été associées à celles obtenues par curation manuelle de la littérature pour construire la première version de l’interactome extracellulaire humain
The extracellular matrix is an intricate tridimensional network supporting cells and a bioactive molecule reservoir involved in the regulation of cell behavior. It is composed of 1027 proteins in humans (Naba et al., Matrix Biol. 2016), including 274 of the core matrisome and 753 associated proteins (growth factors and extracellular matrix regulators) and 6 glycosaminoglycans including 5 sulfated. The extracellular matrix is altered in numerous pathologies (Bonnans et al., Nat. Rev. Mol. Cell Biol. 2014). The lysyl oxidase is responsible for the cross-linking of collagens and elastin and is involved in many cancers. The extracellular matrix is a reservoir of bioactive fragments named matricryptins which are released by proteolysis of extracellular matrix proteins and regulate numerous biological processes like angiogenesis and adipogenesis (Ricard-Blum et Vallet, Matrix Biol. 2017). We have expressed under a recombinant form in human cells some matricryptins including the ectodomains of the membrane collagens XIII, XVII, XXIII and XXV and have identified their extracellular partners. We have characterized the propeptide of lysyl oxidase by SEC-MALS, dynamic light scattering, and SAXS and have built a coarse-grained 3D model by SAXS-derived constraints. We have identified 17 new partners of this fragment and analyzed the mutant Arg158Gln which has no biological activity. This mutation has been identified in humans and inhibits the propeptide anti-proliferative properties. It is associated to an increased risk of breast cancer (Min et al., Cancer Res. 2009). We have expressed the mature lysyl oxidase and modelled its tridimensional structure using available data. All the interactions identified in this study were associated to manually curated interactions described in the literature to build the first version of the human extracellular interactions network
Analyzing how climate change has affected forest growth is crucial for predicting future dynamics and adapting forest management to future climate change. In this paper, we investigate how climate ...change has modified stand dominant height dynamics and site index of 20 European tree species. We used an innovative method based on an annual height increment equation to model stand dominant height as a function of climate back to 1872 and of other stand environmental conditions. We used these models to simulate stand dominant height dynamics and site index under two different climates (prior to climate change and actual recent climate) to analyze the impact of climate change over the past century. To build our models, we combined the recently published FYRE long-term climate database, which provides daily data since 1871, with data from more than 17,000 forest stands of the French National Forest Inventory network. Higher temperature, precipitation and climatic water balance generally favor stand dominant height dynamics when the variables are considered separately. However, the positive effects often saturate at the higher end of the variable distribution. Over the past century, the effect of climate change on the site index has varied widely among species, ranging from a decrease of less than 3% to an increase of more than 5%. The effect of climate change has also varied within species, with more positive effects on initially temperature-limited stands for some species. For the species and environmental conditions considered, our results highlight a positive response of site index to past climate change for most species, albeit with between- and within-species differences. Our results also suggest that this positive response could become negative under continued climate change. These conclusions, as well as the quantitative relationships we provide between climate and stand dominant height dynamics or site index, will help design management strategies to adapt forests to climate change.
•We modeled stand dominant height as a function of annual climate for 20 species.•On average, site index increased over the past century for most species.•Site index varied widely between and within species with climate change.•Site index increased mainly on temperature-limited sites.
The extent to which histone modifying enzymes contribute to DNA methylation in mammals remains unclear. Previous studies suggested a link between the lysine methyltransferase EHMT2 (also known as G9A ...and KMT1C) and DNA methylation in the mouse. Here, we used a model of knockout mice to explore the role of EHMT2 in DNA methylation during mouse embryogenesis. The Ehmt2 gene is expressed in epiblast cells but is dispensable for global DNA methylation in embryogenesis. In contrast, EHMT2 regulates DNA methylation at specific sequences that include CpG-rich promoters of germline-specific genes. These loci are bound by EHMT2 in embryonic cells, are marked by H3K9 dimethylation, and have strongly reduced DNA methylation in Ehmt2(-/-) embryos. EHMT2 also plays a role in the maintenance of germline-derived DNA methylation at one imprinted locus, the Slc38a4 gene. Finally, we show that DNA methylation is instrumental for EHMT2-mediated gene silencing in embryogenesis. Our findings identify EHMT2 as a critical factor that facilitates repressive DNA methylation at specific genomic loci during mammalian development.
In this work, oxidation mechanisms were studied in fine-grained (FG) and coarse-grained (CG) Ti2AlC bulk samples. Results showed that the oxidation kinetics are controlled by the grain size of ...Ti2AlC. Bigger are the grains, faster is the oxidation. A dense and protective Al2O3 layer forms at the surface of FG-Ti2AlC samples while for the CG-Ti2AlC samples, a thick TiO2 layer forms on top of a discontinuous Al2O3. CG-Ti2AlC was observed to simultaneously transform into Ti3AlC2 and TiC instead of being directly transformed into TiC. This transformation result in the following crystallographically sandwich-like structure: (0001) Ti2AlC // (0001) Ti3AlC2 // (111) TiC. The volume shrinkage associated to this transformation produces elongated holes that are partially filled by α-Al2O3. The stress caused by the volume shrinkage generates cracks at the surface, which makes the oxygen inwards diffusion easier and thus worsens the oxidation resistance the CG-Ti2AlC bulk.
This paper presents an approach based on acoustic analysis to describe gender equality in French audiovisual streams, through the estimation of male and female speaking time. Gender detection systems ...based on Gaussian Mixture Models, i-vectors and Convolutional Neural Networks (CNN) were trained using an internal database of 2,284 French speakers and evaluated using REPERE challenge corpus. The CNN system obtained the best performance with a frame-level gender detection F-measure of 96.52 and a hourly women speaking time percentage error bellow 0.6%. It was considered reliable enough to realize large-scale gender equality descriptions. The proposed gender detection system has been packaged as an open-source framework.
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