The evolution of natural competence in Streptococcus pneumoniae

  • Daniel Engelmoer

    Student thesis: Phd


    Naturally competent bacterial species, which self-induce the recombination mechanism of transformation, are wide spread across the bacterial tree-of-life. However, it remains unclear why competence has evolved in these bacteria. Although it is likely that exact explanations will be different for each species, a common selective factor cannot be excluded. Currently, three dominant hypotheses, which focus on the transformation function, try to explain the benefits of competence. Firstly, competence is thought to increase the rate of adaptation by combining beneficial alleles in single genotypes. Secondly, competence can repair DNA-damage by replacing the damaged DNA fragments with undamaged ones. Thirdly, the DNA uptake during competence is used to recycle environmental DNA fragments for nutrients. One of the naturally competent species is the Gram-positive Streptococcus pneumoniae, which is an opportunistic pathogen generally inhabiting the naso-pharyngeal area of young children. Competence in S. pneumoniae is regulated via density dependent extracellular signaling peptide. Here I use a combination of experiments designed around knockout mutants of the signaling mechanism and next-generation sequencing methods to test the first two hypotheses in S. pneumoniae. First, I extend on the DNA-for-repair hypothesis by showing that competent populations of S. pneumoniae are better protected not only against a DNA-damaging agent, but also against protein synthesis inhibitors. However, the mechanisms underlying this protection differ between types of stress. DNA-damage requires the full process of transformation, while protection against protein synthesis inhibitors only requires the activation of the competent cell state. This shows that benefits of competence cannot be totally explained by the benefits of transformation. Second, I use a long-term evolution experiment, where competent and non-competent strains are kept in the presence and absence of periodic stress, to determine the importance of competence for the generation of genetic variation. I find that competence does not increase the rate of adaptation in S. pneumoniae. The fitness of evolved competent populations was significantly lower than those of non-competent populations evolved over the same period of time. However, the intrinsic costs of competence are mitigated by the addition of short periods of stress exposure. These results confirm the prediction of the fitness associated recombination (FAR) hypothesis that competence is favoured in low-fitness situations. Thirdly, whole genome re-sequencing of the evolved populations allowed me to explore genomic evolution next to fitness changes. The genomic data revealed that competence reduces the mutational load of deleterious mutations rather than generating combinations of beneficial alleles. In addition I show several case of parallel genomic evolution within each treatment and across treatments. This shows that parallel evolution is not restricted by genotypic background (competence) or environment (periodic stress). Finally, these results show that competence has evolved in populations of S. pneumoniae as a mechanism to deal with various forms of stress.
    Date of Award1 Aug 2013
    Original languageEnglish
    Awarding Institution
    • The University of Manchester
    SupervisorDaniel Rozen (Supervisor) & Ian Roberts (Supervisor)


    • Whole-genome sequencing
    • Experimental evolution
    • Evolution of sex
    • Streptococcus pneumoniae

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