Insertion sequence-driven evolution of Escherichia coli in chemostats

Joël Gaffé, Christopher McKenzie, Ram P. Maharjan, Evelyne Coursange, Tom Ferenci, Dominique Schneider

Research output: Contribution to journalArticle

34 Citations (Scopus)

Abstract

Insertion sequence (IS) elements are present in almost all bacterial genomes and are mobile enough to provide genomic tools to differentiate closely related isolates. They can be used to estimate genetic diversity and identify fitness-enhancing mutations during evolution experiments. Here, we determined the genomic distribution of eight IS elements in 120 genomes sampled from Escherichia coli populations that evolved in glucose- and phosphate-limited chemostats by comparison to the ancestral pattern. No significant differential transposition of the various IS types was detected across the environments. The phylogenies revealed substantial diversity amongst clones sampled from each chemostat, consistent with the phenotypic diversity within populations. Two IS-related changes were common to independent chemostats, suggesting parallel evolution. One of them corresponded to insertions of IS1 elements within rpoS encoding the master regulator of stress conditions. The other parallel event was an IS5-dependent deletion including mutY involved in DNA repair, thereby providing the molecular mechanism of generation of mutator clones in these evolving populations. These deletions occurred in different co-existing genotypes within single populations and were of various sizes. Moreover, differential locations of IS elements combined with their transpositional activity provided evolved clones with different phenotypic landscapes. Therefore, IS elements strongly influenced the evolutionary processes in continuous E. coli cultures by providing a way to modify both the global regulatory network and the mutation rates of evolving cells.

Original languageEnglish
Pages (from-to)398-412
Number of pages15
JournalJournal of Molecular Evolution
Volume72
Issue number4
DOIs
Publication statusPublished - Apr 2011
Externally publishedYes

Keywords

  • Cell Culture Techniques/instrumentation
  • DNA Transposable Elements
  • Escherichia coli/genetics
  • Evolution, Molecular
  • Gene Rearrangement
  • Genes, Bacterial
  • Genetic Variation
  • Genome, Bacterial
  • Mutation
  • Phylogeny

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  • Cite this

    Gaffé, J., McKenzie, C., Maharjan, R. P., Coursange, E., Ferenci, T., & Schneider, D. (2011). Insertion sequence-driven evolution of Escherichia coli in chemostats. Journal of Molecular Evolution, 72(4), 398-412. https://doi.org/10.1007/s00239-011-9439-2