Mostrando recursos 1 - 20 de 46

  1. Recurrent Reverse Evolution Maintains Polymorphism after Strong Bottlenecks in Commensal Gut Bacteria

    Sousa, Ana; Ramiro, Ricardo S.; Barroso-Batista, João; Güleresi, Daniela; Lourenço, Marta; Gordo, Isabel
    The deposited article is a post-print version and has been submitted to peer review.

  2. Evolution of commensal bacteria in the intestinal tract of mice

    Sousa, Ana; Frazão, Nelson; Ramiro, Ricardo S; Gordo, Isabel
    The deposited article is a post-print version and has been submitted to peer review.

  3. Enhanced Survival of Rifampin- and Streptomycin-Resistant Escherichia coli Inside Macrophages

    Durão, Paulo; Gülereşi, Daniela; Proença, João; Gordo, Isabel
    The deposited article is a post-print version and has been submitted to peer review.

  4. Potential for adaptation overrides cost of resistance

    Moura de Sousa, Jorge; Sousa, Ana; Bourgard, Catarina; Gordo, Isabel
    The deposited article is a post-print version and has been submitted to peer review.

  5. Rates of transposition in Escherichia coli

    Sousa, A.; Bourgard, C.; Wahl, L. M.; Gordo, I.
    The evolutionary role of transposable elements (TEs) is still highly controversial. Two key parameters, the transposition rate (u and w, for replicative and non-replicative transposition) and the excision rate (e) are fundamental to understanding their evolution and maintenance in populations. We have estimated u, w and e for six families of TEs (including eight members: IS1, IS2, IS3, IS4, IS5, IS30, IS150 and IS186) in Escherichia coli, using a mutation accumulation (MA) experiment. In this experiment, mutations accumulate essentially at the rate at which they appear, during a period of 80 500 (1610 generations × 50 lines) generations, and spontaneous...

  6. The evolution of X chromosome inactivation in mammals: the demise of Ohno’s hypothesis?

    Pessia, Eugénie; Engelstädter, Jan; Marais, Gabriel A. B.
    Ohno's hypothesis states that dosage compensation in mammals evolved in two steps: a twofold hyperactivation of the X chromosome in both sexes to compensate for gene losses on the Y chromosome, and silencing of one X (X-chromosome inactivation, XCI) in females to restore optimal dosage. Recent tests of this hypothesis have returned contradictory results. In this review, we explain this ongoing controversy and argue that a novel view on dosage compensation evolution in mammals is starting to emerge. Ohno's hypothesis may be true for a few, dosage-sensitive genes only. If so few genes are compensated, then why has XCI evolved...

  7. RATES OF FITNESS DECLINE AND REBOUND SUGGEST PERVASIVE EPISTASIS

    Perfeito, L.; Sousa, A.; Bataillon, T.; Gordo, I.
    Unraveling the factors that determine the rate of adaptation is a major question in evolutionary biology. One key parameter is the effect of a new mutation on fitness, which invariably depends on the environment and genetic background. The fate of a mutation also depends on population size, which determines the amount of drift it will experience. Here, we manipulate both population size and genotype composition and follow adaptation of 23 distinct Escherichia coli genotypes. These have previously accumulated mutations under intense genetic drift and encompass a substantial fitness variation. A simple rule is uncovered: the net fitness change is negatively...

  8. Evolution of clonal populations approaching a fitness peak

    Gordo, I.; Campos, P. R. A.
    Populations facing novel environments are expected to evolve through the accumulation of adaptive substitutions. The dynamics of adaptation depend on the fitness landscape and possibly on the genetic background on which new mutations arise. Here, we model the dynamics of adaptive evolution at the phenotypic and genotypic levels, focusing on a Fisherian landscape characterized by a single peak. We find that Fisher's geometrical model of adaptation, extended to allow for small random environmental variations, is able to explain several features made recently in experimentally evolved populations. Consistent with data on populations evolving under controlled conditions, the model predicts that mean...

  9. The Genetic Basis of Escherichia coli Pathoadaptation to Macrophages

    Miskinyte, Migla; Sousa, Ana; Ramiro, Ricardo S.; de Sousa, Jorge A. Moura; Kotlinowski, Jerzy; Caramalho, Iris; Magalhães, Sara; Soares, Miguel P.; Gordo, Isabel
    Antagonistic interactions are likely important driving forces of the evolutionary process underlying bacterial genome complexity and diversity. We hypothesized that the ability of evolved bacteria to escape specific components of host innate immunity, such as phagocytosis and killing by macrophages (MΦ), is a critical trait relevant in the acquisition of bacterial virulence. Here, we used a combination of experimental evolution, phenotypic characterization, genome sequencing and mathematical modeling to address how fast, and through how many adaptive steps, a commensal Escherichia coli (E. coli) acquire this virulence trait. We show that when maintained in vitro under the selective pressure of host...

  10. An ABC Method for Estimating the Rate and Distribution of Effects of Beneficial Mutations

    Moura de Sousa, J. A.; Campos, P. R. A.; Gordo, I.
    Determining the distribution of adaptive mutations available to natural selection is a difficult task. These are rare events and most of them are lost by chance. Some theoretical works propose that the distribution of newly arising beneficial mutations should be close to exponential. Empirical data are scarce and do not always support an exponential distribution. Analysis of the dynamics of adaptation in asexual populations of microorganisms has revealed that these can be summarized by two effective parameters, the effective mutation rate, Ue, and the effective selection coefficient of a beneficial mutation, Se. Here, we show that these effective parameters will...

  11. Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages

    Miskinyte, M.; Gordo, I.
    Mutations causing antibiotic resistance usually incur a fitness cost in the absence of antibiotics. The magnitude of such costs is known to vary with the environment. Little is known about the fitness effects of antibiotic resistance mutations when bacteria confront the host's immune system. Here, we study the fitness effects of mutations in the rpoB, rpsL, and gyrA genes, which confer resistance to rifampin, streptomycin, and nalidixic acid, respectively. These antibiotics are frequently used in the treatment of bacterial infections. We measured two important fitness traits-growth rate and survival ability-of 12 Escherichia coli K-12 strains, each carrying a single resistance...

  12. An experimental test on the probability of extinction of new genetic variants

    Chelo, Ivo M.; Nédli, Judit; Gordo, Isabel; Teotónio, Henrique
    In 1927, J.B.S. Haldane reasoned that the probability of fixation of new beneficial alleles is twice their fitness effect. This result, later generalized by M. Kimura, has since become the cornerstone of modern population genetics. There is no experimental test of Haldane's insight that new beneficial alleles are lost with high probability. Here we demonstrate that extinction rates decrease with increasing initial numbers of beneficial alleles, as expected, by performing invasion experiments with inbred lines of the nematode Caenorhabditis elegans. We further show that the extinction rates of deleterious alleles are higher than those of beneficial alleles, also as expected....

  13. Natural Genome Diversity of AI-2 Quorum Sensing in Escherichia coli: Conserved Signal Production but Labile Signal Reception

    Brito, P. H.; Rocha, E. P. C.; Xavier, K. B.; Gordo, I.
    Quorum sensing (QS) regulates the onset of bacterial social responses in function to cell density having an important impact in virulence. Autoinducer-2 (AI-2) is a signal that has the peculiarity of mediating both intra- and interspecies bacterial QS. We analyzed the diversity of all components of AI-2 QS across 44 complete genomes of Escherichia coli and Shigella strains. We used phylogenetic tools to study its evolution and determined the phenotypes of single-deletion mutants to predict phenotypes of natural strains. Our analysis revealed many likely adaptive polymorphisms both in gene content and in nucleotide sequence. We show that all natural strains...

  14. Genome architecture is a selectable trait that can be maintained by antagonistic pleiotropy

    Teresa Avelar, Ana; Perfeito, Lília; Gordo, Isabel; Godinho Ferreira, Miguel
    Chromosomal rearrangements are mutations contributing to both within and between species variation; however their contribution to fitness is yet to be measured. Here we show that chromosomal rearrangements are pervasive in natural isolates of Schizosaccharomyces pombe and contribute to reproductive isolation. To determine the fitness effects of chromosome structure, we constructed two inversions and eight translocations without changing the coding sequence. We show that chromosomal rearrangements contribute to both reproductive success in meiosis and growth rate in mitosis with a strong genotype by environment interaction. These changes are accompanied by alterations in gene expression. Strikingly, we find several examples leading...

  15. Fitness Measurements of Evolved Esherichia coli

    Miskinyte, Migla; Gordo, Isabel
    Bacteria can adapt very rapidly to novel selective pressures. In the transition from commensalism to pathogenicity bacteria have to face and adapt to the host immune system. Specifically, the antagonistic interaction imposed by one of the first line of defense of innate immunity cells, macrophages, on commensal bacteria, such as Escherichia coli (E. coli), can lead to its rapid adaptation. Such adaptation is characterized by the emergence of clones with mutations that allow them to better escape macrophage phagocytosis. Here, we describe how to quantify the amount of fitness increase of bacterial clones that evolved under the constant selective pressure...

  16. Evolution of Escherichia coli to Macrophage Cell Line

    Miskinyte, Migla; Gordo, Isabel
    The genomes of species of Escherichia coli (E. coli) show an extraordinary amount of diversity, which include commensal strains and strains belonging to different pathovars. Many strains of E. coli, which can cause mild or severe pathologies in humans, have a commensal ancestor. Understanding the evolutionary changes that can lead to a transition from commensal to pathogen is an important task, which requires integration of different methodologies. One method is experimental evolution of bacteria, in controlled environments, that mimic some of the selective pressures, likely to be important during the transition to pathogenesis. The success of such a transition will...

  17. Haplodiploidy and the Evolution of Eusociality: Worker Reproduction

    Alpedrinha, João; West, Stuart A.; Gardner, Andy
    This deposit is composed by a publication in which the IGC's authors have had the role of collaboration (it's a collaboration publication). This type of deposit in ARCA is in restrictedAccess (it can't be in open access to the public), and can only be accessed by two ways: either by requesting a legal copy from the author (the email contact present in this deposit) or by visiting the following link: https://www.journals.uchicago.edu/doi/10.1086/671994

  18. Haplodiploidy and the Evolution of Eusociality: Worker Revolution

    Alpedrinha, João; Gardner, Andy; West, Stuart A.
    This deposit is composed by a publication in which the IGC's authors have had the role of collaboration (it's a collaboration publication). This type of deposit in ARCA is in restrictedAccess (it can't be in open access to the public), and can only be accessed by two ways: either by requesting a legal copy from the author (the email contact present in this deposit) or by visiting the following link: https://www.journals.uchicago.edu/doi/10.1086/677283

  19. Escherichia coli adaptation to the gut environment: a constant fight for survival

    Gordo, Isabel; Demengeot, Jocelyne; Xavier, Karina
    LAO/ITQB, FCT.

  20. Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

    Barroso-Batista, João; Demengeot, Jocelyne; Gordo, Isabel
    Co-evolution between the mammalian immune system and the gut microbiota is believed to have shaped the microbiota's astonishing diversity. Here we test the corollary hypothesis that the adaptive immune system, directly or indirectly, influences the evolution of commensal species. We compare the evolution of Escherichia coli upon colonization of the gut of wild-type and Rag2(-/-) mice, which lack lymphocytes. We show that bacterial adaptation is slower in immune-compromised animals, a phenomenon explained by differences in the action of natural selection within each host. Emerging mutations exhibit strong beneficial effects in healthy hosts but substantial antagonistic pleiotropy in immune-deficient mice. This...

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