The effect of metabolic stress on genome stability of a synthetic biology chassis Escherichia coli K12 strain

Jillian M. Couto, Anne McGarrity, Julie Russell, William T. Sloan

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Background: Synthetic organism-based biotechnologies are increasingly being proposed for environmental applications, such as in situ sensing. Typically, the novel function of these organisms is delivered by compiling genetic fragments in the genome of a chassis organism. To behave predictably, these chassis are designed with reduced genomes that minimize biological complexity. However, in these proposed applications it is expected that even when contained within a device, organisms will be exposed to fluctuating, often stressful, conditions and it is not clear whether their genomes will retain stability. Results: Here we employed a chemostat design which enabled us to maintained two strains of E. coli K12 under sustained starvation stress: first the reduced genome synthetic biology chassis MDS42 and then, the control parent strain MG1655. We estimated mutation rates and utilised them as indicators of an increase in genome instability. We show that within 24h the spontaneous mutation rate had increased similarly in both strains, destabilizing the genomes. High rates were maintained for the duration of the experiment. Growth rates of a cohort of randomly sampled mutants from both strains were utilized as a proxy for emerging phenotypic, and by association genetic variation. Mutant growth rates were consistently less than rates in non-mutants, an indicator of reduced fitness and the presence of mildly deleterious mutations in both the strains. In addition, the effect of these mutations on the populations as a whole varied by strain. Conclusions: Overall, this study shows that genome reductions in the MDS42 did not stabilize the chassis under metabolic stress. Over time, this could compromise the effectiveness of synthetic organisms built on chassis in environmental applications.

Original languageEnglish
Article number8
Number of pages10
JournalMicrobial Cell Factories
Volume17
DOIs
Publication statusPublished - 22 Jan 2018

Keywords

  • chassis
  • chemostat
  • environmental biotechnology
  • escherichia coli
  • genome reduction
  • metabolic stress
  • mutation rate
  • synthetic biology

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