Deciphering the Molecular Basis of Wine Yeast Fermentation Traits Using a Combined Genetic and Genomic Approach

The genetic basis of the phenotypic diversity of yeast is still poorly understood. Wine yeast strains have specific abilities to grow and ferment under stressful conditions compared with other strains, but the genetic basis underlying these traits is unknown. Understanding how sequence variation influences such phenotypes is a major challenge to address adaptation mechanisms of wine yeast. We aimed to identify the genetic basis of fermentation traits and gain insight into their relationships with variations in gene expression among yeast strains. We combined fermentation trait QTL mapping and expression profiling of fermenting cells in a segregating population from a cross between a wine yeast derivative and a laboratory strain. We report the identification of QTL for various fermentation traits (fermentation rates, nitrogen utilization, metabolites production) as well as expression QTL (eQTL). We found that many transcripts mapped to several eQTL hotspots and that two of them overlapped with QTL for fermentation traits. A QTL controlling the maximal fermentation rate and nitrogen utilization overlapping with an eQTL hotspot was dissected. We functionally demonstrated that an allele of the ABZ1 gene, localized in the hotspot and involved in p-aminobenzoate biosynthesis, controls the fermentation rate through modulation of nitrogen utilization. Our data suggest that the laboratory strain harbors a defective ABZ1 allele, which triggers strong metabolic and physiological alterations responsible for the generation of the eQTL hotspot. They also suggest that a number of gene expression differences result from some alleles that trigger major physiological disturbances

<i>Staphylococcus aureus </i>Transcriptome Architecture:From Laboratory to Infection-Mimicking Conditions

Staphylococcus aureus is a major pathogen that colonizes about 20% of the human population. Intriguingly, this Gram-positive bacterium can survive and thrive under a wide range of different conditions, both inside and outside the human body. Here, we investigated the transcriptional adaptation of S. aureus HG001, a derivative of strain NCTC 8325, across experimental conditions ranging from optimal growth in vitro to intracellular growth in host cells. These data establish an extensive repertoire of transcription units and non-coding RNAs, a classification of 1412 promoters according to their dependence on the RNA polymerase sigma factors SigA or SigB, and allow identification of new potential targets for several known transcription factors. In particular, this study revealed a relatively low abundance of antisense RNAs in S. aureus, where they overlap only 6% of the coding genes, and only 19 antisense RNAs not co-transcribed with other genes were found. Promoter analysis and comparison with Bacillus subtilis links the small number of antisense RNAs to a less profound impact of alternative sigma factors in S. aureus. Furthermore, we revealed that Rho-dependent transcription termination suppresses pervasive antisense transcription, presumably originating from abundant spurious transcription initiation in this A+T-rich genome, which would otherwise affect expression of the overlapped genes. In summary, our study provides genome-wide information on transcriptional regulation and non-coding RNAs in S. aureus as well as new insights into the biological function of Rho and the implications of spurious transcription in bacteria

Identification of Bacillus subtilis RNA genes using Tiling Arrays

National audienc

Origine des Spécificités Phénotypiques de la Levure œnologique a travers une Approche Génomique

National audienc

Assemblage de génomes bactériens séquencés par NGS - Comparaison d’outils et choix de paramètres

National audience● Les Méthodes de Séquençage de Nouvelle Génération (NGS) permettent de séquencer rapidement et à faible coût de nouvelles souches. → multiplication des outils d’assemblage de NGS (très nombreuses lectures courtes) + évolution rapide des techniques de séquençage. → nécessité de comparer les diverses stratégies d'assemblage sur un jeu de données commun. ● Objectifs de l’étude : → comparer deux stratégies d'assemblage des régions spécifiques. → évaluer diverses méthodes de nettoyage des lectures (l’assembleur de novo choisi ne prenant pas en compte la qualité des données). → déterminer la couverture minimale suffisante lors d’études de détection de nouveaux gènes

Assemblage de génomes bactériens séquencés par NGS - Comparaison d’outils et choix de paramètres

National audience● Les Méthodes de Séquençage de Nouvelle Génération (NGS) permettent de séquencer rapidement et à faible coût de nouvelles souches. → multiplication des outils d’assemblage de NGS (très nombreuses lectures courtes) + évolution rapide des techniques de séquençage. → nécessité de comparer les diverses stratégies d'assemblage sur un jeu de données commun. ● Objectifs de l’étude : → comparer deux stratégies d'assemblage des régions spécifiques. → évaluer diverses méthodes de nettoyage des lectures (l’assembleur de novo choisi ne prenant pas en compte la qualité des données). → déterminer la couverture minimale suffisante lors d’études de détection de nouveaux gènes

Genoscapist: online exploration of quantitative profiles along genomes via interactively customized graphical representations

International audienceGenoscapist is a web-tool generating high-quality images for interactive visualization of hundreds of quantitative profiles along a reference genome together with various annotations. Relevance is demonstrated by deployment of two websites dedicated to large condition-dependent transcriptome datasets available for Bacillus subtilis and Staphylococcus aureus

Assemblage de génomes bactériens séquencés par NGS - Comparaison d’outils et choix de paramètres

National audience● Les Méthodes de Séquençage de Nouvelle Génération (NGS) permettent de séquencer rapidement et à faible coût de nouvelles souches. → multiplication des outils d’assemblage de NGS (très nombreuses lectures courtes) + évolution rapide des techniques de séquençage. → nécessité de comparer les diverses stratégies d'assemblage sur un jeu de données commun. ● Objectifs de l’étude : → comparer deux stratégies d'assemblage des régions spécifiques. → évaluer diverses méthodes de nettoyage des lectures (l’assembleur de novo choisi ne prenant pas en compte la qualité des données). → déterminer la couverture minimale suffisante lors d’études de détection de nouveaux gènes

Constitutive stringent response restores viability of Bacillus subtilis lacking structural maintenance of chromosome protein

Bacillus subtilis mutants lacking the SMC-ScpAB complex are severely impaired for chromosome condensation and partitioning, DNA repair, and cells are not viable under standard laboratory conditions. We isolated suppressor mutations that restored the capacity of a smc deletion mutant (Δsmc) to grow under standard conditions. These suppressor mutations reduced chromosome segregation defects and abrogated hypersensitivity to gyrase inhibitors of Δsmc. Three suppressor mutations were mapped in genes involved in tRNA aminoacylation and maturation pathways. A transcriptomic survey of isolated suppressor mutations pointed to a potential link between suppression of Δsmc and induction of the stringent response. This link was confirmed by (p)ppGpp quantification which indicated a constitutive induction of the stringent response in multiple suppressor strains. Furthermore, sublethal concentrations of arginine hydroxamate (RHX), a potent inducer of stringent response, restored growth of Δsmc under non permissive conditions. We showed that production of (p)ppGpp alone was sufficient to suppress the thermosensitivity exhibited by the Δsmc mutant. Our findings shed new light on the coordination between chromosome dynamics mediated by SMC-ScpAB and other cellular processes during rapid bacterial growth

The GEMO project: Hitchhiking DNA in Magnaporthe oryzae

National audienceMagnaporthe oryzae is a successful pathogen of crop plants and a threat for food production worldwide. This species gathers pathogens of different Poaceae including rice and wheat and causes the main fungal disease of rice worldwide. The Evolutionary Genomics of Magnaporthe oryzae (GEMO) project is an attempt to identify the genomic determinants and evolutionary events involved in pathogenesis, host specificity and adaptation. We have analyzed and compared a dataset of ten closely related genomes of the Magnaporthe oryzae/grisea species complex selected for their different main host and host range. We put emphasis on the horizontally acquired material that we predicted with a parametric detection method based on tetranucleotide signature. We outline the general content of the predicted transferred regions and propose for some candidates the likely taxonomy of their potential donors. We depicted and compared the functional profiles of the host and acquired genes and investigated the intermingling of horizontal transfers with our de novo prediction of transposable elements as a potential adaptative and evolutionary feed. First results pointed out a few large transferred regions potentially acquired from distant species identified by alignment-free methods, including several plant-pathogen fungi. These candidates called for further research around their potential contribution to phenotype, in a step to open the general study of the yet unresolved evolutionary tangram of the Magnaporthe oryzae pathogenesis