Less effective selection leads to larger genomes

International audienceThe evolutionary origin of the striking genome size variations found in eukaryotes remains enigmatic. The effective size of populations, by controlling selection efficacy, is expected to be a key parameter underlying genome size evolution. However, this hypothesis has proved difficult to investigate using empirical datasets. Here, we tested this hypothesis using twenty-two de novo transcriptomes and low-coverage genomes of asellid isopods, which represent eleven independent habitat shifts from surface water to resource-poor groundwater. We show that these habitat shifts are associated with higher transcriptome-wide dN/dS. After ruling out the role of positive selection and pseudogenization, we show that these transcriptome-wide dN/dS increases are the consequence of a reduction in selection efficacy imposed by the smaller effective population size of subterranean species. This reduction is paralleled by an important increase in genome size (25% increase on average), an increase also confirmed in subterranean decapods and mollusks. We also control for an adaptive impact of genome size on life history traits but find no correlation between body size, or growth rate, and genome size. We show instead that the independent increases in genome size measured in subterranean isopods are the direct consequence of increasing invasion rates by repeated elements, which are less efficiently purged out by purifying selection. Contrary to selection efficacy, polymorphism is not correlated to genome size. We propose that recent demographic fluctuations and the difficulty to observe polymorphism variations in polymorphism-poor species can obfuscate the link between effective population size and genome size when polymorphism data is used alone

Clone-Dependent Expression of Esca Disease Revealed by Leaf Metabolite Analysis

Grapevine trutk diseases, especially Esca, are of major concern since they gradually alter vineyards worldwide and cause heavy economic losses. The expression of Esca disease symptoms depends on several factors, including the grapevine cultivar. In this context, a possible clone-dependent expression of the Esca disease was studied. Two clones of ‘Chardonnay’ grown in the same plot were compared according to their developmental and physiological traits, metabolome, and foliar symptom expression. Analysis of their leaf metabolome highlighted differences related to symptom expression. Interestingly, the content of a few specific metabolites exhibited opposite variations in leaves of symptomatic shoots of clones 76 and 95. Altogether this study showed a clone-dependent expression of Esca disease in ‘Chardonnay’ and the relevance of GC-MS and 3D fluorescence methods to analyze the impact of the disease on the leaf metabolome

Adaptation de Staphylococcus aureus à des antimicrobiens ciblant la voie de synthèse des acides gras (FASII)

Staphylococcus aureus est une bactérie pathogène responsable de nombreuses infections communautaires et nosocomiales contre laquelle il est indispensable d'envisager de nouvelles stratégies de traitements du fait de l'émergence de résistances aux antibiotiques. La synthèse bactérienne des acides gras (FASII Fatty Acid Synthesis II) fut proposée comme une nouvelle cible. Cependant, malgré l'enthousiasme suscité par cette approche, sa réalisation est compromise car de nombreux pathogènes à Gram positif peuvent utiliser des acides gras de l'hôte rendant ainsi la voie FASII non essentielle à la croissance bactérienne in vivo. Cependant le statut de S. aureus était encore controversé.S. aureus peut contourner l'inhibition de la voie FASII par deux stratégies. La première consiste à muter des enzymes de l'initiation de FASII, facilitant l'incorporation d'acides gras exogènes. La peau de l'hôte, riche en FA et souvent colonisée par des staphylocoques pourrait constituer une niche favorable au développement de tels mutants lors de l'utilisation ectopique d'un anti-FASII. Nous avons recherché la présence de ce type de résistance dans des souches cliniques et montré que les FA augmentaient de 58% le taux de résistance dans un échantillonnage de 700 isolats. De plus, les substitutions facilitant le contournement de la voie FASII mise en évidence in vitro ont été retrouvées dans des isolats naturels. La seconde stratégie consiste en une adaptation non mutationnelle qui implique une phase de « dormance » après laquelle S. aureus s'est affranchi de sa voie FASII et est capable d'incorporer les FA. L'adaptation mutationnelle est stable alors qu'en l'absence de mutation, la résistance est réversible. Nous avons montré l'importance du stress cellulaire dans l'adaptation et une corrélation entre l'adaptation et des changements de l'enveloppe bactérienne. Enfin, nous avons réalisé une analyse RNAseq qui constituera une base de données utile à de futurs travaux. En conclusion, dans l'état actuel des connaissances, le traitement d'infections staphylococciques par des inhibiteurs de FASII n'est pas souhaitable car leur effet peut être contourné par mutation et/ou par adaptation. Cependant, il est possible qu'une combinaison entre un anti-FASII et d'autres cibles métaboliques ait un effet synergique.Staphylococcus aureus is a major cause of hospital and community acquired infections of major concern due to the increasing rate of antibiotic resistance, making the development of new treatments a priority. One target actively developed over several years is the fatty acid (FA) synthesis (FASII) pathway. However, despite widespread publicity of this strategy, it is deeply compromised, as numerous Gram positive pathogens use exogenous FA, as available in the host, making FASII nonessential for growth in vivo. Nevertheless, the status of S. aureus remained controversial.The main result of this work is that S. aureus overrides FASII inhibition by two strategies: the first involves high frequency mutations in FASII initiation enzymes, which facilitate exogenous FA incorporation. Such mutants may be selected on skin when exposed to FASII inhibitors, as skin is often colonized by staphylococci and is FA-rich. We searched for the presence of such resistance in clinical isolates and found that FA increased resistance frequencies by 58 % in a screen of 700 clinical isolates. Importantly, the point substitutions allowing FASII bypass described in vitro are present among natural isolates. The second strategy involves adaptation without detectable mutation, in which S. aureus undergoes transient "dormancy", followed by a FASII-bypass-proficient state. Mutational adaptation is stable, whereas non-mutational adaptation is reversible. We demonstrated the importance of stress and found that FASII bypass is favored when stress is reduced. We showed that FASII bypass is accompanied by envelope changes and we performed an RNAseq analysis that will serve as a database for future studies. We conclude that in its present state, FASII inhibition is not a suitable strategy for treating staphylococcal infections, as a FASII block can be bypassed by mutation and/or adaptation. However, our data also suggest that major physiological changes during treatment may lead to essentiality of a different gene set, a finding that might be used to develop a combinatorial drug approach. We propose that anti-FASII drugs might be used in association with other antibiotics (to be identified) that could lead to a synergistic anti-S. aureus effect

Modelisation des proprietes magnetiques et des fluctuations de charge dans les systemes etendus: extension du modele des fonctions de Bloch

SIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : TD 78298 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

L'opportunité du Supply Chain Rating (SCR) : un examen de la sensibilité du consommateur à l'éco-performance de chaîne

International audienceL'opacité de fonctionnement au sein de supply chains (SC) fragmentées, et l'opportunisme qui en résulte, expliquent pour une large part les nombreux scandales industriels dans tous les secteurs (Guérin et al., 2014). Partant de ce constat, et en excluant le statu quo, nous envisageons dans le cadre du projet de recherche CLASSE (cofinancé FEDER/ Région Normandie), l'option stratégique reposant sur la mise en place d'une nouvelle dynamique au sein des supply chains initiée grâce à l'arbitrage contraignant de consommateurs plus informés et plus sensibilisés à l'éco-performance. Cette seconde voie décrit une démarche que l'on qualifiera ici de Supply Chain Rating (SCR) qui suppose la production d'information sur le fonctionnement des chaînes logistiques (SC). A travers notre projet de recherche, nous proposons l'analyse de la faisabilité de la mise en œuvre d'un SCR à destination des consommateurs intégrant en priorité des critères d'efficience économique et d'efficience environnementale (écologique), dits alors d'éco-performance.</p

L'opportunité du Supply Chain Rating (SCR) : un examen de la sensibilité du consommateur à l'éco-performance de chaîne

International audienceL'opacité de fonctionnement au sein de supply chains (SC) fragmentées, et l'opportunisme qui en résulte, expliquent pour une large part les nombreux scandales industriels dans tous les secteurs (Guérin et al., 2014). Partant de ce constat, et en excluant le statu quo, nous envisageons dans le cadre du projet de recherche CLASSE (cofinancé FEDER/ Région Normandie), l'option stratégique reposant sur la mise en place d'une nouvelle dynamique au sein des supply chains initiée grâce à l'arbitrage contraignant de consommateurs plus informés et plus sensibilisés à l'éco-performance. Cette seconde voie décrit une démarche que l'on qualifiera ici de Supply Chain Rating (SCR) qui suppose la production d'information sur le fonctionnement des chaînes logistiques (SC). A travers notre projet de recherche, nous proposons l'analyse de la faisabilité de la mise en œuvre d'un SCR à destination des consommateurs intégrant en priorité des critères d'efficience économique et d'efficience environnementale (écologique), dits alors d'éco-performance.</p

Oxygen response and tolerance mechanisms in Clostridioides difficile

International audienceWhile the gut is typically thought of as anoxic, there are two intersecting and decreasing oxygen gradients that are observed in the gut: oxygen decreases from the small to the large intestine and from the intestinal epithelium toward the colon lumen. Gut oxygen levels also increase following antibiotic induced-dysbiosis. While dysbiosis favors growth of Clostridioides difficile, the oxygen increase also causes stress to this anaerobic enteropathogen. To circumvent oxygen threat, C. difficile has developed efficient strategies: sporulation, biofilm formation, the rerouting of central metabolism and the production of oxygen detoxification enzymes. Especially, reverse rubrerythrins and flavodiiron proteins involved in oxygen reduction are crucial in C. difficile ability to tolerate and survive the oxygen concentrations encountered in the gastrointestinal tract. Two regulators, σB and PerR, play pivotal role in the mastering of these adaptive responses by controlling the various systems that protect cells from oxidative damages

Improved protoplast yield and cell wall regeneration in Gracilaria verrucosa (Huds.) Papenfuss (Gracilariales, Rhodophyta)

International audienc

Assessment of Bona Fide sRNAs in Staphylococcus aureus

Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches