“Ant” and “Grasshopper” Life-History Strategies in Saccharomyces cerevisiae

From the evolutionary and ecological points of view, it is essential to distinguish between the genetic and environmental components of the variability of life-history traits and of their trade-offs. Among the factors affecting this variability, the resource uptake rate deserves particular attention, because it depends on both the environment and the genetic background of the individuals. In order to unravel the bases of the life-history strategies in yeast, we grew a collection of twelve strains of Saccharomyces cerevisiae from different industrial and geographical origins in three culture media differing for their glucose content. Using a population dynamics model to fit the change of population size over time, we estimated the intrinsic growth rate (r), the carrying capacity (K), the mean cell size and the glucose consumption rate per cell. The life-history traits, as well as the glucose consumption rate, displayed large genetic and plastic variability and genetic-by-environment interactions. Within each medium, growth rate and carrying capacity were not correlated, but a marked trade-off between these traits was observed over the media, with high K and low r in the glucose rich medium and low K and high r in the other media. The cell size was tightly negatively correlated to carrying capacity in all conditions. The resource consumption rate appeared to be a clear-cut determinant of both the carrying capacity and the cell size in all media, since it accounted for 37% to 84% of the variation of those traits. In a given medium, the strains that consume glucose at high rate have large cell size and low carrying capacity, while the strains that consume glucose at low rate have small cell size but high carrying capacity. These two contrasted behaviors may be metaphorically defined as “ant” and “grasshopper” strategies of resource utilization. Interestingly, a strain may be “ant” in one medium and “grasshopper” in another. These life-history strategies are discussed with regards to yeast physiology, and in an evolutionary perspective

Niche-driven evolution of metabolic and life-history strategies in natural and domesticated populations of Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Variation of resource supply is one of the key factors that drive the evolution of life-history strategies, and hence the interactions between individuals. In the yeast <it>Saccharomyces cerevisiae</it>, two life-history strategies related to different resource utilization have been previously described in strains from different industrial origins. In this work, we analyzed metabolic traits and life-history strategies in a broader collection of yeast strains sampled in various ecological niches (forest, human body, fruits, laboratory and industrial environments).</p> <p>Results</p> <p>By analysing the genetic and plastic variation of six life-history and three metabolic traits, we showed that <it>S. cerevisiae </it>populations harbour different strategies depending on their ecological niches. On one hand, the forest and laboratory strains, referred to as extreme "ants", reproduce quickly, reach a large carrying capacity and a small cell size in fermentation, but have a low reproduction rate in respiration. On the other hand, the industrial strains, referred to as extreme "grasshoppers", reproduce slowly, reach a small carrying capacity but have a big cell size in fermentation and a high reproduction rate in respiration. "Grasshoppers" have usually higher glucose consumption rate than "ants", while they produce lower quantities of ethanol, suggesting that they store cell resources rather than secreting secondary products to cross-feed or poison competitors. The clinical and fruit strains are intermediate between these two groups.</p> <p>Conclusions</p> <p>Altogether, these results are consistent with a niche-driven evolution of <it>S. cerevisiae</it>, with phenotypic convergence of populations living in similar habitat. They also revealed that competition between strains having contrasted life-history strategies ("ants" and "grasshoppers") seems to occur at low frequency or be unstable since opposite life-history strategies appeared to be maintained in distinct ecological niches.</p

Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

International audienceBackground: The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana

Systemic properties of metabolic networks lead to an epistasis-based model for heterosis

The genetic and molecular approaches to heterosis usually do not rely on any model of the genotype–phenotype relationship. From the generalization of Kacser and Burns’ biochemical model for dominance and epistasis to networks with several variable enzymes, we hypothesized that metabolic heterosis could be observed because the response of the flux towards enzyme activities and/or concentrations follows a multi-dimensional hyperbolic-like relationship. To corroborate this, we used the values of systemic parameters accounting for the kinetic behaviour of four enzymes of the upstream part of glycolysis, and simulated genetic variability by varying in silico enzyme concentrations. Then we “crossed” virtual parents to get 1,000 hybrids, and showed that best-parent heterosis was frequently observed. The decomposition of the flux value into genetic effects, with the help of a novel multilocus epistasis index, revealed that antagonistic additive-by-additive epistasis effects play the major role in this framework of the genotype–phenotype relationship. This result is consistent with various observations in quantitative and evolutionary genetics, and provides a model unifying the genetic effects underlying heterosis

Variabilité du protéome enzymatique et contrôle métabolique (vers un modèle biochimique de l'hétérosis)

Décrit et exploité depuis plus de deux siècles l'hétérosis reste un phénomène mal compris. Pour étudier ses manifestations au niveau biochimique, nous nous sommes appuyés sur une explication de la dominance issue de la théorie du contrôle métabolique, qui stipule une relation de type hyperbolique entre l'activité d'une enzyme d'une chaîne et le flux. Mon travail de thèse a consisté à généraliser cette approche, en considérant plusieurs enzymes variables, et en imposant une contrainte sur la concentration totale d'enzymes allouée à la chaîne. Après avoir montré, par simulation, que le flux des hybrides pouvait être hétérotique, j'ai cherché à confirmer expérimentalement ce modèle. Pour cela, j'ai reconstitué in vitro la première partie de la glycolyse, et " mimé " la variabilité génétique en faisant varier les concentrations des enzymes. Chaque tube représentait donc un " génotype parental " et les " hybrides " étaient obtenus par simple mélange du contenu de tubes parentaux. Ce système a permis de proposer une méthode de caractérisation systémique des activités enzymatiques, et de déduire les concentrations optimum des enzymes. Il aussi permis de confirmer le modèle d'hétérosis biochimique en intégrant à la fois dominance et superdominance. La dernière partie de ma thèse a consisté à étudier par simulation le flux glycolytique chez Saccharomyces cerevisiae. Les paramètres cinétiques du modèle avaient été estimés in vivo, et j'ai estimé les concentrations des enzymes par protéomique quantitative. J'ai ainsi pu simuler un très grand nombre de croisements, et montrer que les résultats obtenus sur une chaîne réelle concordaient avec ceux obtenus sur le système in vitro.Described for more than two centuries, and largely used by breeders, heterosis remains a poorly understood phenomenon. In order to study its biochemical bases, we relied on an explanation of dominance derived from metabolic control theory, in which the relationship between the activity of one enzyme and the flux trough the pathway is hyperbolic. The purpose of my Thesis was to generalise this approach, by taking into account several enzymes, and considering a global constraint on the total enzyme content of the pathway. First I showed by simulation that the flux of hybrids could display heterosis, and then I tested experimentally the validity of this prediction. I reconstituted in vitro the upper part of glycolysis, and "mimicked" the genetic variability by varying the concentrations of enzymes. Each tube corresponded to a "parental" genotype, and the glycolytic flux to phenotype. Mixing the content of parental tubes generated "hybrids". This system allowed me to propose a method to characterize systemic enzyme activities, and to deduce the optimum distribution of enzyme concentrations. On the other hand, it fully confirmed the biochemical model for heterosis, which integrated both dominance and overdominance genetic models. The last part of my Thesis focused on simulations of glycolytic flux in Saccharomyces cerevisiae. The kinetic parameters of the model had been estimated in vivo, and I have estimated the concentrations of the enzymes by quantitative proteomics. Thus, I have simulated a large number of crosses, and showed that the results on an actual pathway are consistent with the results obtained in vitro.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

Les populations expérimentales de cartographie génétique

International audienceA l'âge vénérable de près d'un siècle, la cartographie génétique reste une approche centrale en biologie, à laquelle on a recours dans des contextes variés, et avec des objectifs très différents : analyse de l'organisation des génomes (duplications, inversions, etc.), cartographie comparée (étude de la conservation de la synténie entre différentes espèces), cartographie de QTL (Quantitative Trait Loci) et de eQTL (QTL d’expression), génétique d’association, isolement de gènes (positional cloning), SAM (sélection assistée par marqueurs), etc. Les populations génétiques utilisées, dont le choix répond à des objectifs spécifiques, se sont diversifiées, surtout depuis que l'on dispose de marqueurs moléculaires en nombre quasiment illimité. Il n'est pas toujours facile de s'y retrouver parce que les croisements mis en œuvre sont variés et que, ces populations ayant été développées indépendamment chez les végétaux et les rongeurs de laboratoires, le vocabulaire associé diffère souvent entre les deux domaines. Cette note fait le point sur la terminologie des populations expérimentales les plus courantes, leur mode d'obtention, leurs particularités et leurs intérêts

Structuration de la diversité métabolique chez escherichia coli (Intégration du réseau métabolique, du protéome, des paramètres enzymatiques et des phénotypes de croissance)

Les microorganismes sont remarquablement adaptés à des environnements divers, changeants et imprévisibles. Escherischia coli est une bactérie d'importance en santé publique et compte parmi les plus versatiles. Sa diversité génétique intra-spécifique a été très étudiée et indique l'existence d'une plasticité du génome et d'une structure en phylogroupes. Alors que le métabolisme détermine la capacité d'une bactérie à exploiter les ressources, la diversité métabolique de l'espèce est mal connue. Pour comprendre le rôle des facteurs écologiques dans l'évolution de cette espèce, nous avons étudié l'importance et la structure de la diversité pour trois caractères métaboliques : la présence/absence de réactions au sein du réseau métabolique, la capacité à utiliser différentes sources de carbone et la variation des concentrations des protéines dans différents milieux. Nous avons montré que les réseaux métaboliques partagent un large noyau de réactions communes, et que leur part variable est structurée en fonction de la phylogénie. Toutefois, les phénotypes métaboliques ne sont pas liés aux phylogroupes et E. coli constitue un unique groupe phénotypique, ce qui suggère l'absence de spécialisation pour l'utilisation de source de carbone. Ce travail révèle l'importance de la diversité métabolique intra-spécifique et suggère de nouvelles hypothèses à propos des relations génotype/phénotype. La diversité métabolique intra-spécifique étant très structurée par les ressources en interaction avec les souches mais peu par la phylogénie de l'espèce ou le mode de vie, elle pourrait brouiller le signal phylogénétique. En perspective, l'intégration des données expérimentales dans les modèles métaboliques permettrait de mettre en relation les concentrations des enzymes avec les taux de croissance.Microorganisms are remarkably adapted to diverse, changing and unpredictable environments. Although metabolism is directly linked to the bacterial ability to grow in an ecological niche, the intra-species metabolic diversity is poorly known. Escherichia coli is one of the most versatile medically important species. Its intra-species genetic diversity has been thoroughly studied showing its genome plasticity and phylogroup structure. In order to better understand the role of ecological factors in the species evolution, we studied the extent and structure of metabolic diversity throughout the species for three metabolic traits: the presence/absence of reactions in the metabolic networks, the ability to grow on different carbon sources and the variation of protein concentrations in different environments. We found that metabolic networks share a large core of common reactions, and that its variable part is structured according to the species phylogeny. Nevertheless, metabolic phenotypes are not linked to phylogroups and E. coli constitutes a single phenotypic group, which suggests that no specialization occurred for carbon source usage within the species. This work reveals the extent of the intra-species metabolic diversity and suggests new hypotheses about genotype-phenotype relationships that could blur the phylogenetic signal. The main emerging picture is that the intra-species metabolic diversity is highly structured by the resources in interaction with the strains but weakly by the strain phylogeny or lifestyle. Further prospects consist in integrating these experimental data into metabolic models to relate variation of enzyme concentrations to growth rates.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF

The Pitfalls of Heterosis Coefficients

Heterosis (hybrid vigour) is a universal phenomenon of crucial agro-economic and evolutionary importance. We show that the most common heterosis coefficients do not properly measure deviation from additivity because they include both a component accounting for &ldquo;real&rdquo; heterosis and a term that is not related to heterosis, since it is derived solely from parental values. Therefore, these coefficients are inadequate whenever the aim of the study is to compare heterosis levels between different traits, environments, genetic backgrounds, or developmental stages, as these factors may affect not only the level of non-additivity, but also parental values. The only relevant coefficient for such comparisons is the so-called &ldquo;potence ratio&rdquo;. Because most heterosis studies consider several traits/stages/environmental conditions, our observations support the use of the potence ratio, at least in non-agronomic contexts, because it is the only non-ambiguous heterosis coefficient