GMGM - Génétique moléculaire, génomique, microbiologie - Université de Strasbourg https://gmgm.unistra.fr fr GMGM - Génétique moléculaire, génomique, microbiologie - Université de Strasbourg Sun, 04 Dec 2022 03:29:46 +0100 Sun, 04 Dec 2022 03:29:46 +0100 TYPO3 EXT:news news-12803 Tue, 29 Nov 2022 13:50:18 +0100 Un ARN pour détecter le fluor ouvrant la porte vers le développement d’enzymes de dépollution /actualites/actualite/un-arn-pour-detecter-le-fluor-ouvrant-la-porte-vers-le-developpement-denzymes-de-depollution Retrouvez la dernière publication (doi.org/10.1002/smll.202205232) de Claire HUSSER et de Michael RYCKELYNCK (équipe « Biologie Digitale de l’ARN ») en ligne sur le site du journal Small. Ce travail, réalisé en collaboration avec Stéphane VUILLEUMIER (équipe “Adaptations et interactions des microorganismes dans l’environnement”, GMGM, Université de Strasbourg – CNRS), présente le développement de « FluorMango », un biosenseur ARN capable d’émettre une fluorescence exclusivement en présence d’ion fluorure. Cette molécule est le premier biosenseur permettant de détecter de façon directe, dynamique et biocompatible la présence de fluorure. Les auteurs ont ainsi pu mesurer en temps réel la dégradation d’un composé fluoré (le fluoracétate) par l’activité enzymatique contenue dans des cellules vivantes. Réalisé dans le cadre du projet ANR « MicroFluor », ce développement est un pas important vers la découverte de nouvelles enzymes de dépollution par criblage fonctionnel de populations microbiennes issues d’échantillons environnementaux ou de banque de gènes. Parmi les activités cibles, des enzymes capables des dégrader les Substances Alkyl (Poly)Perfluorées (PFAS), une large famille de composés extrêmement stables et toxiques, produits industriellement en grandes quantités et retrouvés de manière croissante dans l’environnement.

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Actualités du GMGM Actualités de l'Équipe Vuilleumier
news-12783 Thu, 24 Nov 2022 11:04:58 +0100 Article dans le magazine Savoir(s) : Une bactérie pour manger un médicament antidiabétique, micropolluant de l’environnement. /actualites/actualite/une-bacterie-pour-manger-un-medicament-antidiabetique-micropolluant-de-lenvironnement-article-dans-savoirs

Au-delà des polluants majeurs comme les hydrocarbures et les solvants, notre mode de vie diffuse dans l’environnement des polluants pharmaceutiques, appelés micropolluants en raison des concentrations très faibles auxquelles ils sont rencontrés, que les stations d’épuration parviennent encore mal à éliminer. En s’intéressant à cette problématique, l’équipe de Stéphane Vuilleumier, chercheur au laboratoire de Génétique moléculaire, génomique, microbiologie (GMGM – CNRS / Unistra), est parvenue à isoler une bactérie capable de se nourrir d'un des agents antidiabétiques les plus prescrits au monde, la metformine.

 

Article de Savoir(s) : Une bactérie pour manger un médicament antidiabétique, micropolluant de l’environnement

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Actualités du GMGM Actualités de l'Équipe Vuilleumier
news-12772 Tue, 22 Nov 2022 13:44:34 +0100 Nouvelle publication équipe AIME : une bactérie se nourrissant de metformine, antidiabétique et contaminant aquatique majeur /actualites/actualite/nouvelle-publication-equipe-aime-une-bacterie-se-nourrissant-de-metformine-antidiabetique-et-contaminant-aquatique-majeur A Methylotrophic Bacterium Growing with the Antidiabetic Drug, Metformin as Its Sole Carbon, Nitrogen and Energy Source. Chaignaud, Gruffaz, et al. Microorganisms 2022, 10, 2302. https://doi.org/10.3390/microorganisms10112302 La metformine est un médicament de première intention contre le diabète de type II et l'un des agents antidiabétiques les plus prescrits dans le monde (150 millions de personnes). Il est également envisagé pour d'autres applications thérapeutiques, y compris le cancer et les troubles endocriniens. La metformine reste largement non métabolisée par les enzymes humaines. À des doses quotidiennes de 0,5 à 2,5 g par patient, il est devenu un micropolluant dominant dans les stations d'épuration des eaux usées et les milieux aquatiques. Ses effets toxiques sont encore débattus, avec des effets néfastes signalés chez les organismes aquatiques et potentiellement aussi chez l'homme.
 Les micro-organismes sont ici en première ligne, avec leur capacité à développer la capacité de transformer enzymatiquement les contaminants chimiques, et de tolérer leurs effets toxiques. Le métabolisme microbien des composés à un atome de carbone ou dépourvus de liaisons carbone-carbone est à même de jouer un rôle-clé dans la dégradation de nombreux produits pharmaceutiques tels que la metformine, dont les atomes de carbone sont exclusivement liés à des atomes d'autres éléments.
 À notre connaissance, aucun micro-organisme capable d'utiliser la metformine comme source de carbone et d'azote pour la croissance n'avait encore été signalé. Nous décrivons ici la souche Aminobacter niigataensis MD1, une bactérie méthylotrophe aérobie capable d'utiliser la metformine comme seule source de carbone, d'azote et d'énergie pour sa croissance et isolée à partir de boues activées de la station d'épuration de la Ville de Strasbourg. Le génome de la souche MD1 a été séquencé, son métabolisme de la metformine a été étudié en détail par transcriptomique et protéomique, et les gènes impliqués dans la croissance avec la metformine ont été identifiés. Les résultats obtenus suggèrent une évolution récente de la capacité de la souche MD1 à dégrader la metformine pour sa croissance.

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Actualités du GMGM Actualités de l'Équipe Vuilleumier
news-12765 Mon, 21 Nov 2022 15:40:05 +0100 MITO team : editorial in Frontiers Physiology /actualites/actualite/mito-team-editorial-in-frontiers-physiology Editorial for a special issue of Frontiers Physiology Burzio VA, Barrey E, Leucci E, Entelis N,
Hollander JM and Das S (2022)
Editorial:
Role of mitochondria-associated noncoding
RNAs inintracellular communication.
Front. Physiol. 13:980674.
doi: 10.3389/fphys.2022.980674
 

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Entelis - Tarassov Publications de l'Équipe Entelis - Tarassov
news-12713 Mon, 14 Nov 2022 11:05:46 +0100 New publication of the MITO team in Computational and Structural Biotechnology Journal /actualites/actualite/new-publication-of-the-mito-team-in-computational-and-structural-biotechnology-journal Theoretical and mathematical biology paper about hub-centred RNA-protein networks Smirnov A (2022) How global RNA-binding proteins coordinate the behaviour of RNA regulons: an information approach. Comput Struct Biotechnol J doi:10.1016/j.csbj.2022.11.019

RNA-binding proteins are central players in post-transcriptional regulation. Some of them, such as the well-studied bacterial RNA chaperones Hfq and ProQ or the eukaryotic RNAi factor Argonaute, interact with hundreds-to-thousands of different RNAs and thereby globally affect gene expression. As a shared yet limited resource, these and other RNA-binding hubs drive strong competition between their multiple ligands. This creates a ground for significant cross-communication between RNA targets, which enables them to share information, “synchronise” their behaviour, and produce interesting biochemical effects, sometimes propagating across the highly connected RNA-protein network. This property is likely universally present in hub-centred networks and plays a key role in global gene expression programmes. It is also an important factor in biotechnology and synthetic biology applications of RNA/protein-based circuits. However, few studies so-far focused on describing and explaining this phenomenon from first principles. Here we introduce an information theory-based framework to comprehensively and exactly describe information flow in hub-centred networks. We show that information sharing can achieve significant levels in relatively small networks, provided the hub is present in limiting concentrations. The transmitted information is sufficient to noticeably affect the binding probabilities of competing targets but drops exponentially along the network. Target overexpression can disrupt communication between other targets, while hub sequestration boosts the crosstalk. We also find that overlaps between the interactomes of two different hubs create both entropic challenges and new forms of long-range communication between RNAs and proteins.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Entelis - Tarassov Publications de l'Équipe Entelis - Tarassov
news-12686 Fri, 04 Nov 2022 14:43:28 +0100 Fête de la Science 2022 à Lingolsheim /actualites/actualite/fete-de-la-science-2022-a-lingolsheim La Fête de la Science s'est déroulée du 7 au 9 octobre 2022 à Lingolsheim https://www.fetedelascience.fr/village-des-sciences-de-lingolsheim Découvrez le monde fascinant de la recherche à travers des ateliers et des conférences:

- environnement: le monde des abeilles et de l'apithérapie

- santé humaine: la levure de boulanger pour mieux comprendre les maladies génétiques rares

- un autre regard sur l'Art: comment on perçoit une œuvre d'art grâce à l'application Ikonikat

- le monde de l'ARN: construisez de l'ARN avec des bases aimantées

- biodiversité: les champignons filamenteux, les observer et les comprendre

- chimie: façonner les molécules pour en faire des micro-machines

- orientation: découvrir les métiers de la recherche scientifique au CNRS

- 2022 Année du Bicentenaire de la naissance de Louis Pasteur: Louis Pasteur microbiologiste

- Comité du Bas-Rhin de La Ligue contre le cancer (Ligue 67): la recherche contre le cancer, L’Agenda scolaire (ma santé, j’en prends soin), comment se protéger du cancer

- Sciences participatives: Avec le jeu Mendeleieva, découvrez les éléments chimiques de votre vie de tous les jours et des femmes scientifiques étudiant ces éléments.

3 équipes du GMGM ont tenu des strands lors de cet évennement.

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Actualités du GMGM Actualités de l'Équipe Becker Actualités de l'Équipe Friant Actualités de l'Équipe Vuilleumier
news-12541 Mon, 10 Oct 2022 08:54:49 +0200 Nouvelle publication dans Molecular Biology and Evolution /actualites/actualite/nouvelle-publication-dans-molecular-biology-and-evolution-1 Loss of heterozygosity spectrum depends on ploidy level in natural yeast populations.
Abhishek Dutta, Fabien Dutreux, Joseph Schacherer.
Molecular Biology and Evolution. 2022. doi:10.1093/molbev/msac214

The appearance of genomic variations such as loss of heterozygosity (LOH) has a significant impact on phenotypic diversity observed in a population. Recent large-scale yeast population genomic surveys have shown a high frequency of these events in natural isolates and more particularly in polyploids. However, the frequency, extent, and spectrum of LOH in polyploid organisms have never been explored and is poorly characterized to date. Here, we accumulated 5,163 LOH events over 1,875 generations in 76 mutation accumulation (MA) lines comprising nine natural heterozygous diploid, triploid, and tetraploid natural S. cerevisiae isolates from different ecological and geographical origins. We found that the rate and spectrum of LOH are variable across ploidy levels. Of the total accumulated LOH events, 8.5%, 21%, and 70.5% of them were found in diploid, triploid, and tetraploid MA lines, respectively. Our results clearly shows that the frequency of generated LOH events increases with ploidy level. In fact, the cumulative LOH rates were estimated to be 9.3×10−3, 2.2×10−2, and 8.4×10−2 events per division for diploids, triploids, and tetraploids, respectively. In addition, a clear bias towards the accumulation of interstitial and short LOH tracts is observed in triploids and tetraploids compared to diploids. The variation of the frequency and spectrum of LOH events across ploidy level could be related to the genomic instability, characterizing higher ploidy isolates.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-12383 Thu, 08 Sep 2022 10:55:44 +0200 Nouvelle publication dans PNAS /actualites/actualite/nouvelle-publication-dans-pnas Loss-of-function mutation survey revealed that genes with background-dependent fitness are rare and functionally related in yeast.
Elodie Caudal, Anne Friedrich, Arthur Jallet, Marion Garin, Jing Hou, Joseph Schacherer.
Proc Natl Acad Sci U S A. 2022. doi:10.1073/pnas.2204206119

In natural populations, the same mutation can lead to different phenotypic outcomes due to the genetic variation that exists among individuals. Such genetic background effects are commonly observed, including in the context of many human diseases. However, systematic characterization of these effects at the species level is still lacking to date. Here, we sought to comprehensively survey background-dependent traits associated with gene loss-of-function (LoF) mutations in 39 natural isolates of Saccharomyces cerevisiae using a transposon saturation strategy. By analyzing the modeled fitness variability of a total of 4,469 genes, we found that 15% of them, when impacted by a LoF mutation, exhibited a significant gain- or loss-of-fitness phenotype in certain natural isolates compared with the reference strain S288C. Out of these 632 genes with predicted background-dependent fitness effects, around 2/3 impact multiple backgrounds with a gradient of predicted fitness change while 1/3 are specific to a single genetic background. Genes related to mitochondrial function are significantly overrepresented in the set of genes showing a continuous variation and display a potential functional rewiring with other genes involved in transcription and chromatin remodeling as well as in nuclear–cytoplasmic transport. Such rewiring effects are likely modulated by both the genetic background and the environment. While background-specific cases are rare and span diverse cellular processes, they can be functionally related at the individual level. All genes with background-dependent fitness effects tend to have an intermediate connectivity in the global genetic interaction network and have shown relaxed selection pressure at the population level, highlighting their potential evolutionary characteristics.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-12382 Thu, 08 Sep 2022 10:49:45 +0200 Nouvelle publication /actualites/actualite/nouvelle-publication Extensive simulations assess the performance of genome-wide association mapping in various Saccharomyces cerevisiae subpopulations.
Jackson Peter, Anne Friedrich, Gianni Liti, Joseph Schacherer.
Philosophical Proceedings of the Royal Society B. 2022. doi:10.1098/rstb.2020.0514

With the advent of high throughput sequencing technologies, genome-wide association studies (GWAS) have become a powerful paradigm for dissecting the genetic origins of the observed phenotypic variation. We recently completely sequenced the genome of 1011 Saccharomyces cerevisiae isolates, laying a strong foundation for GWAS. To assess the feasibility and the limits of this approach, we performed extensive simulations using five selected subpopulations as well as the total set of 1011 genomes. We measured the ability to detect the causal genetic variants involved in Mendelian and more complex traits using a linear mixed model approach. The results showed that population structure is well accounted for and is not the main problem when the sample size is high enough. While the genetic determinant of a Mendelian trait is easily mapped in all studied subpopulations, discrepancies are seen between datasets when performing GWAS on a complex trait in terms of detection, false positive and false negative rate. Finally, we performed GWAS on the different defined subpopulations using a real quantitative trait (resistance to copper sulfate) and showed the feasibility of this approach. The performance of each dataset depends simultaneously on several factors such as sample size, relatedness and population evolutionary history.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-12102 Tue, 07 Jun 2022 15:28:00 +0200 Chaires juniors dans le domaine de recherches sur les mitochondries /actualites/actualite/chaires-juniors-dans-le-domaine-de-recherches-sur-les-mitochondries Le Laboratoire d'excellence (LabEx) MitoCross annonce l'appel aux candidatures de deux chaires juniors dans le domaine de recherches sur les mitochondries. Voir les détails ICI.

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Actualités du GMGM Actualités de l'Équipe Becker Actualités de l'Équipe Entelis - Tarassov Actualités de l'Équipe Schacherer
news-12082 Thu, 02 Jun 2022 15:48:19 +0200 Prix du meilleur poster pour Louis-François Mey /actualites/actualite/prix-du-meilleur-poster-pour-louis-francois-mey Louis-François MEY, doctorant dans l'équipe AIME, a obtenu le prix du meilleur poster pour son travail "Experimental evolution of methylotrophic strains for growth with chloromethane" lors de la conférence "Microbial Cycling of Volatile Organic Compounds: Biogeochemistry to Biotechnology" qui s'est tenue à Norwich (UK) les 25 et 26 mai 2022.

 

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Actualités du GMGM Actualités de l'Équipe Vuilleumier
news-12039 Tue, 24 May 2022 15:47:50 +0200 Nouvelle publication dans Environmental Microbiome /actualites/actualite/nouvelle-publication-dans-environmental-microbiome A putatively new family of alphaproteobacterial chloromethane degraders from a deciduous forest soil revealed by stable isotope probing and metagenomics.
Eileen Kröber, Saranya Kanukollu, Sonja Wende, Françoise Bringel, Steffen Kolb
Environ Microbiome. 2022;17(1):24. doi: 10.1186/s40793-022-00416-2.

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Actualités du GMGM Actualités de l'Équipe Vuilleumier
news-11998 Fri, 13 May 2022 09:29:52 +0200 Chapitre d'ouvrage /actualites/actualite/chapitre-douvrage RNA interference (RNAi) as a tool for high-resolution phenotypic screening of the pathogenic yeast Candida glabrata. Andreas Tsouris, Joseph Schacherer, Olena P. Ishchuk. Yeast Functional Genomics. 2022. doi:10.1007/978-1-0716-2257-5_18 RNA interference (RNAi) as a tool for high-resolution phenotypic screening of the pathogenic yeast Candida glabrata.
Andreas Tsouris, Joseph Schacherer, Olena P. Ishchuk.
Yeast Functional Genomics. 2022. doi:10.1007/978-1-0716-2257-5_18

After its discovery RNA interference (RNAi) has become a powerful tool to study gene functions in different organisms. RNAi has been applied at genome-wide scale and can be nowadays performed using high-throughput automated systems (robotics). The simplest RNAi process requires the expression of two genes (Dicer and Argonaute) to function. To initiate the silencing, constructs generating either double-strand RNA or antisense RNA are required. Recently, RNAi was reconstituted by expressing Saccharomyces castellii genes in the human pathogenic yeast Candida glabrata and was used to identify new genes related to the virulence of this pathogen. In this chapter, we describe a method to make the C. glabrata pathogenic yeast competent for RNAi and to use RNA silencing as a tool for low- or high-resolution phenotypic screening in this species.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-11165 Mon, 02 May 2022 17:05:27 +0200 Nouvelle publication dans Genomics /actualites/actualite/nouvelle-publivation-dans-genomics Towards accurate, contiguous and complete alignment-based polyploid phasing algorithms.
Omar Abou Saada, Anne Friedrich, Joseph Schacherer.
Genomics. 2022. doi:10.1016/j.ygeno.2022.110369

Phasing, and in particular polyploid phasing, have been challenging problems held back by the limited read length of high-throughput short read sequencing methods which can't overcome the distance between heterozygous sites and labor high cost of alternative methods such as the physical separation of chromosomes for example. Recently developed single molecule long-read sequencing methods provide much longer reads which overcome this previous limitation. Here we review the alignment-based methods of polyploid phasing that rely on four main strategies: population inference methods, which leverage the genetic information of several individuals to phase a sample; objective function minimization methods, which minimize a function such as the Minimum Error Correction (MEC); graph partitioning methods, which represent the read data as a graph and split it into k haplotype subgraphs; cluster building methods, which iteratively grow clusters of similar reads into a final set of clusters that represent the haplotypes. We discuss the advantages and limitations of these methods and the metrics used to assess their performance, proposing that accuracy and contiguity are the most meaningful metrics. Finally, we propose the field of alignment-based polyploid phasing would greatly benefit from the use of a well-designed benchmarking dataset with appropriate evaluation metrics. We consider that there are still significant improvements which can be achieved to obtain more accurate and contiguous polyploid phasing results which reflect the complexity of polyploid genome architectures.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-11007 Wed, 06 Apr 2022 11:18:47 +0200 Participation de Françoise Bringel de l'équipe AIME à l'édition 2022 d'Ose la recherche /actualites/actualite/participation-de-francoise-bringel-de-lequipe-aime-a-ledition-2022-dose-la-recherche Une rencontre entre scientifiques, jeunes curieux de 14 et 16 ans et parents (https://www.levaisseau.com/fr/familles/ose-la-recherche/) co-organisée entre la Collectivité européenne d’Alsace, par le biais de son établissement le Vaisseau, et la délégation Alsace du CNRS, avec le soutien de l’Académie de Strasbourg.

Visiter la liste des portraits des chercheurs en  biologie ayant participé en cliquant sur le lien : https://www.levaisseau.com/IMG/pdf/fiches_metiers_OLR_2019-2020_2021_biologie_web.pdf

 

 

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news-10978 Thu, 31 Mar 2022 20:52:54 +0200 Nouvelle publication dans Molecular Ecology /actualites/actualite/nouvelle-publication-dans-molecular-ecology Brettanomyces bruxellensis: overview of the genetic and phenotypic diversity of an anthropized yeast.
Jules Harrouard, Chris Eberlein, Patricia Ballestra, Marguerite Dols-Lafargue, Isabelle Masneuf-Pomarede, Cécile Miot-Sertier, Joseph Schacherer, Warren Albertin.
Molecular Ecology. 2022. doi: 10.1111/mec.16439

Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation because of their small genome, short generation time, and their colonization of contrasting and ever-changing ecological niches. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be uncovered. Population genomic studies have revealed the co-existence of auto- and allotriploidization events with different evolutionary outcomes. The different diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation events to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing lownutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels to improve our understanding of an anthropized yeast’s phenotypic landscape.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-10977 Thu, 31 Mar 2022 14:59:11 +0200 Première publication de Emilie Geersens en première auteure !!! /actualites/actualite/publication-de-emilie-geersens  

 

 

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Actualités du GMGM Actualités de l'Équipe Vuilleumier Publications de l'Équipe Vuilleumier
news-10812 Sun, 06 Mar 2022 16:39:28 +0100 Nouvelle publication dans Nature Ecology & Evolution /actualites/actualite/nouvelle-publication-dans-nature-ecology-evolution Domestication reprogrammed the budding yeast life cycle. Domestication reprogrammed the budding yeast life cycle.
Matteo De Chiara, Benjamin P Barré, Karl Persson, Agurtzane Irizar, Chiara Vischioni, Sakshi Khaiwal, Simon Stenberg, Onyetugo Chioma Amadi, Gašper Žun , Katja Doberšek, Cristian Taccioli, Joseph Schacherer, Uroš Petrovič, Jonas Warringer, Gianni Liti.


Domestication of plants and animals is the foundation for feeding the world human population but can profoundly alter the biology of the domesticated species. Here we investigated the effect of domestication on one of our prime model organisms, the yeast Saccharomyces cerevisiae, at a species-wide level. We tracked the capacity for sexual and asexual reproduction and the chronological life span across a global collection of 1,011 genome-sequenced yeast isolates and found a remarkable dichotomy between domesticated and wild strains. Domestication had systematically enhanced fermentative and reduced respiratory asexual growth, altered the tolerance to many stresses and abolished or impaired the sexual life cycle. The chronological life span remained largely unaffected by domestication and was instead dictated by clade-specific evolution. We traced the genetic origins of the yeast domestication syndrome using genome-wide association analysis and genetic engineering and disclosed causative effects of aneuploidy, gene presence/absence variations, copy number variations and single-nucleotide polymorphisms. Overall, we propose domestication to be the most dramatic event in budding yeast evolution, raising questions about how much domestication has distorted our understanding of the natural biology of this key model species.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-10810 Sun, 06 Mar 2022 14:53:01 +0100 Nouvelle publication dans Current Biology /actualites/actualite/new-publication-in-current-biology Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts. Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts.
Omar Abou Saada, Andreas Tsouris, Chris Large, Anne Friedrich, Maitreya J Dunham, Joseph Schacherer.

Yeasts, and in particular Saccharomyces cerevisiae, have been used for brewing beer for thousands of years. Population genomic surveys highlighted that beer yeasts are polyphyletic, with the emergence of different domesticated subpopulations characterized by high genetic diversity and ploidy level. However, the different origins of these subpopulations are still unclear as reconstruction of polyploid genomes is required. To gain better insight into the differential evolutionary trajectories, we sequenced the genomes of 35 Saccharomyces cerevisiae isolates coming from different beer-brewing clades, using a long-read sequencing strategy. By phasing the genomes and using a windowed approach, we identified three main beer subpopulations based on allelic content (European dominant, Asian dominant, and African beer). They were derived from different admixtures between populations and are characterized by distinctive genomic patterns. By comparing the fully phased genes, the most diverse in our dataset are enriched for functions relevant to the brewing environment such as carbon metabolism, oxidoreduction, and cell wall organization activity. Finally, independent domestication, evolution, and adaptation events across subpopulations were also highlighted by investigating specific genes previously linked to the brewing process. Altogether, our analysis based on phased polyploid genomes has led to new insight into the contrasting evolutionary history of beer isolates.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-10753 Tue, 22 Feb 2022 10:13:31 +0100 Publication Equipe Bahram et Equipe Friant /actualites/actualite/publication-equipe-bahram-et-equipe-friant A Homozygous Missense Variant in PPP1R1B/DARPP-32 Is Associated With Generalized Complex Dystonia. Amjad Khan, Anne Molitor, Sylvain Mayeur, Gaoqun Zhang, Bruno Rinaldi, Béatrice Lannes, Benoît Lhermitte, Muhammad Umair, Stefan T Arold, Sylvie Friant, Sepand Rastegar, Mathieu Anheim, Seiamak Bahram, Raphael Carapito.

Background: The dystonias are a heterogeneous group of hyperkinetic disorders characterized by sustained or intermittent muscle contractions that cause abnormal movements and/or postures. Although more than 200 causal genes are known, many cases of primary dystonia have no clear genetic cause.

Objectives: To identify the causal gene in a consanguineous family with three siblings affected by a complex persistent generalized dystonia, generalized epilepsy, and mild intellectual disability.

Methods: We performed exome sequencing in the parents and two affected siblings and characterized the expression of the identified gene by immunohistochemistry in control human and zebrafish brains.

Results: We identified a novel missense variant (c.142G>A (NM_032192); p.Glu48Lys) in the protein phosphatase 1 regulatory inhibitor subunit 1B gene (PPP1R1B) that was homozygous in all three siblings and heterozygous in the parents. This gene is also known as dopamine and cAMP-regulated neuronal phosphoprotein 32 (DARPP-32) and has been involved in the pathophysiology of abnormal movements. The uncovered variant is absent in public databases and modifies the conserved glutamate 48 localized close to the serine 45 phosphorylation site. The PPP1R1B protein was shown to be expressed in cells and regions involved in movement control, including projection neurons of the caudate-putamen, substantia nigra neuropil, and cerebellar Purkinje cells. The latter cells were also confirmed to be positive for PPP1R1B expression in the zebrafish brain.

Conclusions: We report the association of a PPP1R1B/DARPP-32 variant with generalized dystonia in man. It might be relevant to include the sequencing of this new gene in the diagnosis of patients with otherwise unexplained movement disorders. © 2021 International Parkinson and Movement Disorder Society.

 

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Actualités du GMGM Actualités de l'Équipe Friant Publications de l'Équipe Friant
news-10728 Thu, 17 Feb 2022 14:56:37 +0100 2 sujets de thèse dans l'équipe AIME /actualites/actualite/2-sujets-de-these-dans-lequipe-aime 2 sujets de thèse financés par des contrats ANR sont proposés par l'équipe AIME :

 

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Actualités du GMGM Actualités de l'Équipe Vuilleumier
news-10721 Wed, 16 Feb 2022 15:59:13 +0100 Poste MCF (CNU 65) au concours 2022 dans l'équipe AIME /actualites/actualite/poste-mcf-dans-lequipe-aime Un poste de Maître de conférences en microbiologie "Mécanismes microbiens de réponse aux contaminants chimiques et écotoxicologie microbienne" sera ouvert cette année à l'Université de Strasbourg dans l'équipe Adaptations et Interactions Microbiennes dans l'Environnement (UMR7156).

 

Profil

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Actualités du GMGM Actualités de l'Équipe Vuilleumier
news-10570 Wed, 12 Jan 2022 11:27:09 +0100 New publication of the MITO team in Nucleic Acids Research /actualites/actualite/new-publication-of-the-mito-team-in-nucleic-acids-research-1 Efficient target cleavage by Type V Cas12a effectors programmed with split CRISPR RNA

 

Nucleic Acids Res. 2021 Dec 24. pii: gkab1227. doi: 10.1093/nar/gkab1227. Online ahead of print.

Regina Shebanova 1Natalia Nikitchina 1 2Nikita Shebanov 1Vladimir Mekler 3Konstantin Kuznedelov 3Egor Ulashchik 4Ruslan Vasilev 5 6Olga Sharko 4Vadim Shmanai 4Ivan Tarassov 2Konstantin Severinov 1 3 7Nina Entelis 2Ilya Mazunin 1

 

Abstract

CRISPR RNAs (crRNAs) that direct target DNA cleavage by Type V Cas12a nucleases consist of constant repeat-derived 5'-scaffold moiety and variable 3'-spacer moieties. Here, we demonstrate that removal of most of the 20-nucleotide scaffold has only a slight effect on in vitro target DNA cleavage by a Cas12a ortholog from Acidaminococcus sp. (AsCas12a). In fact, residual cleavage was observed even in the presence of a 20-nucleotide crRNA spacer moiety only. crRNAs split into separate scaffold and spacer RNAs catalyzed highly specific and efficient cleavage of target DNA by AsCas12a in vitro and in lysates of human cells. In addition to dsDNA target cleavage, AsCas12a programmed with split crRNAs also catalyzed specific ssDNA target cleavage and non-specific ssDNA degradation (collateral activity). V-A effector nucleases from Francisella novicida (FnCas12a) and Lachnospiraceae bacterium (LbCas12a) were also functional with split crRNAs. Thus, the ability of V-A effectors to use split crRNAs appears to be a general property. Though higher concentrations of split crRNA components are needed to achieve efficient target cleavage, split crRNAs open new lines of inquiry into the mechanisms of target recognition and cleavage and may stimulate further development of single-tube multiplex and/or parallel diagnostic tests based on Cas12a nucleases.

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Actualités du GMGM Actualités de l'Équipe Entelis - Tarassov Publications de l'Équipe Entelis - Tarassov
news-10301 Wed, 27 Oct 2021 08:28:58 +0200 L’équipe AIME obtient le financement de deux projets ANR cette année !!! /actualites/actualite/lequipe-aime-obtient-le-financement-de-deux-projets-anr-cette-annee Deux projets ANR pilotés par l’équipe AIME ont été financés dans le cadre de l’AAPG2021.

Le premier, intitulé « Discovery and selection of novel defluorinases for bioremediation (MICROFLUOR) », est coordonné par Stéphane VUILLEUMIER, avec pour partenaire l’équipe de Michaël RYCKELYNCK (Equipe "Digital Biology of RNA", IBMC, Strasbourg). Il a pour but d'appliquer la microfluidique de pointe pour la découverte et la sélection de nouveaux catalyseurs pour la dégradation de substances polyfluoroalkylées (PFAS) récalcitrantes.

Le deuxième projet, intitulé « Cruising the marine halomethane cycle: Microbiology, biochemistry and geochemistry of reference bacteria, new microbial players and underlying processes (MAHABIO) », est un projet franco-allemand coordonné par Thierry NADALIG, en partenariat avec Agnès HIRSCHLER (Univ. Aix-Marseille), Frank KEPPLER (Univ. de Heidelberg) et Matthias Boll (Univ. de Freiburg). Ce projet propose un effort interdisciplinaire concerté pour découvrir et caractériser la diversité microbienne et les processus qui sous-tendent la production et la consommation marine de chlorométhane, le composé halogéné le plus abondant dans l'atmosphère terrestre, et contribuer à mieux comprendre le cycle biogéochimique global des halogènes sur notre planète.

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Actualités du GMGM Actualités de l'Équipe Vuilleumier Publications de l'Équipe Vuilleumier
news-10225 Thu, 07 Oct 2021 10:42:00 +0200 Fête de la science 8 au 10 octobre 2021 Illkich La Villa /actualites/actualite/fete-de-la-science-8-au-10-octobre-illkich-la-villa-1 L'équipe Friant et Becker ont tenu un stand à la Fête de la science 8 au 10 octobre 2021 à Illkich à La Villa A programme : Levures et expression de gènes humains

Comment utiliser des levures pour leur faire produire des gènes humains

Observations :

- au microscope,

- de cultures levures de différentes souches,

- comparaison entre souches Saccharomyces cerevisiae, levure de boulangerie, portant un gène sauvage ou des variants de patients atteints de maladies rares,

- boites de Petri avec des tests d'activité de différents produits issus des abeilles

https://www.fetedelascience.fr/la-recherche-sur-le-campus-d-illkirch-couleurs-microbiologie-biodiversite-et-environnement

 

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Actualités du GMGM Actualités de l'Équipe Friant
news-9944 Thu, 24 Jun 2021 09:06:34 +0200 Nouvelle publication (ANR/DFG CHLOROFILTER) /actualites/actualite/nouvelle-publication-anr-dfg-chlorofilter L'équipe AIME a publié un article dans la revue Environmental Microbiology dans le cadre du projet ANR/DFG CHLOROFILTER

13 C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern.

Kröber E, Wende S, Kanukollu S, Buchen-Tschiskale C, Besaury L, Keppler F, Vuilleumier S, Kolb S, Bringel F. Environ Microbiol. doi: 10.1111/1462-2920.15638. PMID: 34121306

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Actualités du GMGM Publications du GMGM Publications de l'Équipe Vuilleumier
news-10347 Thu, 15 Apr 2021 16:31:00 +0200 Publication Equipe Friant et Becker : CEX1 /actualites/actualite/publication-equipe-friant-et-becker-cex1 New publication : Cex1 is a component of the COPI intracellular trafficking machinery Ludovic Enkler, Bruno Rinaldi, Johan Owen de Craene, Philippe Hammann, Osamu Nureki, Bruno Senger, Sylvie Friant, Hubert D Becker

 

COPI (coatomer complex I) coated vesicles are involved in Golgi-to-ER and intra-Golgi trafficking pathways, and mediate retrieval of ER resident proteins. Functions and components of the COPI-mediated trafficking pathways, beyond the canonical set of Sec/Arf proteins, are constantly increasing in number and complexity. In mammalian cells, GORAB, SCYL1 and SCYL3 proteins regulate Golgi morphology and protein glycosylation in concert with the COPI machinery. Here, we show that Cex1, homologous to the mammalian SCYL proteins, is a component of the yeast COPI machinery, by interacting with Sec27, Sec28 and Sec33 (Ret1/Cop1) proteins of the COPI coat. Cex1 was initially reported to mediate channeling of aminoacylated tRNA outside of the nucleus. Our data show that Cex1 localizes at membrane compartments, on structures positive for the Sec33 α-COP subunit. Moreover, the Wbp1 protein required for N-glycosylation and interacting via its di-lysine motif with the Sec27 β'-COP subunit is mis-targeted in cex1Δ deletion mutant cells. Our data point to the possibility of developing Cex1 yeast-based models to study neurodegenerative disorders linked to pathogenic mutations of its human homologue SCYL1.

Biology Open 2021 10: bio058528 doi: 10.1242/bio.058528 Published 22 March 2021

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Becker Actualités de l'Équipe Friant
news-9600 Tue, 06 Apr 2021 09:26:00 +0200 Cex1 is a component of the COPI intracellular trafficking machinery /actualites/actualite/cex1-is-a-component-of-the-copi-intracellular-trafficking-machinery

Ludovic Enkler, Bruno Rinaldi, Johan Owen de Craene, Philippe Hammann, Osamu Nureki, Bruno Senger, Sylvie Friant, Hubert D Becker

COPI (coatomer complex I) coated vesicles are involved in Golgi-to-ER and intra-Golgi trafficking pathways, and mediate retrieval of ER resident proteins. Functions and components of the COPI-mediated trafficking pathways, beyond the canonical set of Sec/Arf proteins, are constantly increasing in number and complexity. In mammalian cells, GORAB, SCYL1 and SCYL3 proteins regulate Golgi morphology and protein glycosylation in concert with the COPI machinery. Here, we show that Cex1, homologous to the mammalian SCYL proteins, is a component of the yeast COPI machinery, by interacting with Sec27, Sec28 and Sec33 (Ret1/Cop1) proteins of the COPI coat. Cex1 was initially reported to mediate channeling of aminoacylated tRNA outside of the nucleus. Our data show that Cex1 localizes at membrane compartments, on structures positive for the Sec33 ?-COP subunit. Moreover, the Wbp1 protein required for N-glycosylation and interacting via its di-lysine motif with the Sec27 ?'-COP subunit is mis-targeted in cex1? deletion mutant cells. Our data point to the possibility of developing Cex1 yeast-based models to study neurodegenerative disorders linked to pathogenic mutations of its human homologue SCYL1.

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Actualités du GMGM
news-9599 Fri, 12 Mar 2021 10:28:00 +0100 Françoise Bringel (équipe AIME) répond à une journaliste de l'Humanité /actualites/actualite/francoise-bringel-equipe-aime-repond-a-une-journaliste-de-lhumanite La journaliste Anna Musso a organisé une table ronde sur la question « Qu’en est-il de la place des femmes dans la recherche ? » avec une double page parue en kiosque le 5-7 mars 2021 dans le journal l’Humanité. Trois questions posées à trois femmes dans des champs disciplinaires différents comme l’astrophysique (Françoise Combes), la physicochimie (Marie-Paule Pileni) et la microbiologie (Françoise Bringel, équipe AIME).  

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Actualités du GMGM Actualités de l'Équipe Vuilleumier
news-9598 Fri, 26 Feb 2021 16:06:00 +0100 L'équipe Friant retenue pour le projet PHC Tassili 2021 /actualites/actualite/lequipe-friant-retenue-pour-le-projet-phc-tassili-2021 Utilisation de modèles animaux et cellulaire pour évaluer les effets in vivo d'une exposition chronique à des pesticides seuls et en cocktails.

Le partenariat Hubert Curien (PHC) Tassili est un programme de coopération algéro-français qui apporte un soutien à des projets de recherche conjoints sur une durée de 3 ans. Le financement porte notamment sur la mobilité au sein de laboratoires français, de jeunes doctorants algériens et d'enseignants pour une habilitation d'une part, et de la mobilité de chercheurs français et algériens entre la France et l'Algérie d'autre part.

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Actualités du GMGM Actualités de l'Équipe Friant