Dynamique et évolution d'ORFs dupliquées chez les levures hémiascomycètes (Etude de la famille multigénique DUP)

STRASBOURG-Sc. et Techniques (674822102) / SudocSudocFranceF

Expansion and contraction of the DUP240 multigene family in Saccharomyces cerevisiae populations.

The influence of duplicated sequences on chromosomal stability is poorly understood. To characterize chromosomal rearrangements involving duplicated sequences, we compared the organization of tandem repeats of the DUP240 gene family in 15 Saccharomyces cerevisiae strains of various origins. The DUP240 gene family consists of 10 members of unknown function in the reference strain S288C. Five DUP240 paralogs on chromosome I and two on chromosome VII are arranged as tandem repeats that are highly polymorphic in copy number and sequence. We characterized DNA sequences that are likely involved in homologous or nonhomologous recombination events and are responsible for intra- and interchromosomal rearrangements that cause the creation and disappearance of DUP240 paralogs. The tandemly repeated DUP240 genes seem to be privileged sites of gene birth and death

An evolutionary scenario for one of the largest yeast gene families.

The DUP gene family of Saccharomyces cerevisiae comprises 23 members that can be divided into two subfamilies--DUP240 and DUP380. The location of the DUP loci suggests that at least three mechanisms were responsible for their genomic dispersion: nonreciprocal translocation at chromosomal ends, tandem duplication and Ty-associated duplication. The data we present here suggest that these nonessential genes encode proteins that facilitate membrane trafficking processes. Dup240 proteins have three conserved domains (C1, C2 and C3) and two predicted transmembrane segments (H1 and H2). A direct repetition of the C1-H1-H2-C2 module is observed in Dup380p sequences. In this article, we propose an evolutionary model to account for the emergence of the two gene subfamilies.journal articleresearch support, non-u.s. gov't2006 Jan2005 11 02importe

Paleogenomics or the search for remnant duplicated copies of the yeast DUP240 gene family in intergenic areas.

Duplication, resulting in gene redundancy, is well known to be a driving force of evolutionary change. Gene families are therefore useful targets for approaching genome evolution. To address the gene death process, we examined the fate of the 10-member-large S288C DUP240 family in 15 Saccharomyces cerevisiae strains. Using an original three-step method of analysis reported here, both slightly and highly degenerate DUP240 copies, called pseudo-open reading frames (ORFs) and relics, respectively, were detected in strain S288C. It was concluded that two previously annotated ORFs correspond, in fact, to pseudo-ORFs and three additional relics were identified in intergenic areas. Comparative intraspecies analysis of these degenerate DUP240 loci revealed that the two pseudo-ORFs are present in a nondegenerate state in some other strains. This suggests that within a given gene family different loci are the target of the gene erasure process, which is therefore strain dependent. Besides, the variable positions observed indicate that the relic sequence may diverge faster than the flanking regions. All in all, this study shows that short conserved protein motifs provide a useful tool for detecting and accurately mapping degenerate gene remnants. The present results also highlight the strong contribution of comparative genomics for gene relic detection because the possibility of finding short conserved protein motifs in intergenic regions (IRs) largely depends on the choice of the most closely related paralog or ortholog. By mapping new genetic components in previously annotated IRs, our study constitutes a further refinement step in the crucial stage of genome annotation and provides a strategy for retracing ancient chromosomal reshaping events and, hence, for deciphering genome history.historical articlejournal articleresearch support, non-u.s. gov't2005 Sep2005 05 25importe

Représentations du sens linguistique 5

National audienceCe volume propose une sélection des contributions présentées à la cinquième édition de la conférence internationale Représentations du sens linguistique, qui s'est tenue à Chambéry du 25 au 27 mai 2011.L'objectif de ces rencontres est de réunir, à la lumière des études existantes, des propositions testables sur la nature du sens linguistique, qui avancent des explications d'une question empirique bien définie, à partir d'outils notionnels pouvant être utilisés dans différents cadres théoriques. On contribue ainsi à répondre aux questions de la nature des représentations sémantiques, des régularités dont elles rendent compte. Ces réponses éclairent la question de la nature des contraintes et représentations que doit intérioriser un locuteur pour maîtriser les différents aspects relevant de la sémantique d'une langue et du langage

Représentations du sens linguistique 5

Cet ouvrage réunit une sélection des contributions présentées à la 5e édition de la conférence internationale "Représentations du sens linguistique" qui s'est tenue à Chambéry du 25 au 27 mai 2011.Sous la direction de Dominique Lagorgette, Pierre Larrivée.Les auteurs remercient le LABEX ASLAN (ANR-10-LABX-0081) de l'Université de Lyon pour son soutien financier dans le cadre du programme "Investissements d'Avenir" (ANR-11-IDEX-0007) de l'Etat Français géré par l'Agence Nationale de la Recherche (ANR).Appartient à la collection : Langages, ISSN 1952-0891 ; 14.National audienceCe volume propose une sélection des contributions présentées à la cinquième édition de la conférence internationale Représentations du sens linguistique, qui s'est tenue à Chambéry du 25 au 27 mai 2011. L'objectif de ces rencontres est de réunir, à la lumière des études existantes, des propositions testables sur la nature du sens linguistique, qui avancent des explications d'une question empirique bien définie, à partir d'outils notionnels pouvant être utilisés dans différents cadres théoriques. On contribue ainsi à répondre aux questions de la nature des représentations sémantiques, des régularités dont elles rendent compte. Ces réponses éclairent la question de la nature des contraintes et représentations que doit intérioriser un locuteur pour maîtriser les différents aspects relevant de la sémantique d'une langue et du langage. SOMMAIRE -*- Introduction / Dominique Lagorgette & Pierre Larrivée --A-- REPRESENTATION DE L'ORALITE EN DIACHRONIE DU FRANCAIS -1- Le discours direct au Moyen Âge : vers une définition et une méthodologie d'analyse / Céline Guillot, Alexei Lavrentiev, Bénédicte Pincemin, Serge Heiden -2- Représentation de l'oral et syntaxe dans la prose de la "Queste del saint Graal" (1225-1230) / Julie Glikman et Nicolas Mazziotta -3- De Estienne Husson pour ce qu'il dit à Jannon Morelot : 'un filz de bastarde ne me puet valoir!' : représentation de l'oral dans les documents comptables médiévaux / Aude Wirth-Jaillard -4- "Ha ! las, fet il, com sui iriez !" : les emplois de "(hé+) las(se)" et l'expression de la douleur morale en français médiéval / Evelyne Oppermann-Marsaux -5- La reformulation des requêtes dans quelques textes littéraires médiévaux / Corine Denoyelle -6- Si voirement con ge sui voir creant : ' voirement ' dans les formules de serment et de prière de l'ancien français / Amalia Rodriguez Somolinos --B-- SESSION GENERALE -7- "Je te baptise", exemplaires et conditions performatives / René-Joseph Lavie -8- Description polyphonique d'un marqueur d'attitude énonciative : carrément / Laurence Rouanne -9- De la prosodie à la syntaxe. Vers une description sémantico-syntaxique des périodes intonatives binaires / Noalig Tanguy -10- Prendre un taureau par les cornes et le mener par le bout du nez. La préhension d'une entité par une de ses parties / Estelle Moline -11- Quelques remarques à propos des phrases prédicationnelles / Fayssal Tayalati --C-- POLYPHONIE -12- Organisation énonciative du discours théâtral. Rôle des points de vue dans la construction de la cohérence textuelle/polyphonique dans "Les Grandes chaleurs" d'Eugène Ionesco / Raluca Bălăită -13- Corps réel et positions énonciatives en langue des signes française / Annie Risler -14- Accords et désaccords : construction des points de vue dans l'émission de cinéma Le Cercle / Marion Sandré et Arnaud Richard -15- L'analyse interactive de textes monologaux choisis sur l'exemple de l'avant-propos / Anna Kieliszczyk -16- L'allusion socioculturelle : un procédé rhétorique complexe pour la co-construction de l'évènement médiatique / Natalia Solovei -17- 'Europe' entre continent et vision politique : l'interprétation du nom propre modifié dans un corpus de discours politique / Anje Müller Gjesdal -18- La linguistique de corpus comme instrument de validation des hypothèses interprétatives : la source des implicatures conversationnelles avec la quantification existentielle / Pierre Larrivée

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga.

Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873), and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex

Genome evolution in yeasts.

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. The hemiascomycete yeasts, with their compact genomes, similar lifestyle and distinct sexual and physiological properties, provide a unique opportunity to explore such mechanisms. We present here the complete, assembled genome sequences of four yeast species, selected to represent a broad evolutionary range within a single eukaryotic phylum, that after analysis proved to be molecularly as diverse as the entire phylum of chordates. A total of approximately 24,200 novel genes were identified, the translation products of which were classified together with Saccharomyces cerevisiae proteins into about 4,700 families, forming the basis for interspecific comparisons. Analysis of chromosome maps and genome redundancies reveal that the different yeast lineages have evolved through a marked interplay between several distinct molecular mechanisms, including tandem gene repeat formation, segmental duplication, a massive genome duplication and extensive gene loss