Genomic plasticity of pathogenic Escherichia coli mediates D-serine tolerance via multiple adaptive mechanisms

Nicky O'Boyle, James P. R. Connolly, Nicholas P. Tucker, Andrew J. Roe

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Abstract

The molecular environment of the host can have profound effects on the behavior of resident bacterial species. We recently established how the sensing and response of enterohaemorrhagic Escherichia coli (EHEC) to D-serine (D-ser) resulted in down regulation of type 3 secretion system dependent colonization, thereby avoiding unfavorable environments abundant in this toxic metabolite. However, this model ignores a key determinant of the success of bacterial pathogens – adaptability. In this study, we have explored adaptation of EHEC to D-ser and its consequences for pathogenesis. We isolated naturally-occurring tolerant EHEC mutants, whose growth was no longer compromised in the presence of D-ser. These mutants arose rapidly within the population and were positively selected for. Strikingly, these mutants overcame both growth inhibition and also the repression of colonization normally associated with D-ser. Through a combination of whole genome sequencing and transcriptomics, we resolved the molecular basis of the tolerance phenotypes. Disruption of the inner membrane D-ser transporter CycA was observed with a mutation resulting in premature termination of translation. Disruption of D-ser transport was exacerbated in some mutants by knockdown in transcription of a second D-ser transporter, SstT. Tolerant mutants without disruption of D-ser transporters exhibited activation of the previously non-functional D-ser deaminase DsdA via an upstream genomic deletion that resulted in constitutive activity via a new promoter. These adaptations highlight the importance of genomic plasticity in the evolution of pathogenic bacteria and demonstrate how mechanistically distinct genetic adaptations can converge to promote common phenotypes.
Original languageEnglish
Number of pages10
JournalProceedings of the National Academy of Sciences of the United States of America
DOIs
Publication statusPublished - 26 Aug 2020

Keywords

  • D-serine
  • Escherichia coli
  • pathogens

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