Synthetic Genome Defenses against Selfish DNA Elements Stabilize Engineered Bacteria against Evolutionary Failure

ACS Synth Biol. 2019 Mar 15;8(3):521-531. doi: 10.1021/acssynbio.8b00426. Epub 2019 Feb 15.


Mobile genetic elements drive evolution by disrupting genes and rearranging genomes. Eukaryotes have evolved epigenetic mechanisms, including DNA methylation and RNA interference, that silence mobile elements and thereby preserve the integrity of their genomes. We created an artificial reprogrammable epigenetic system based on CRISPR interference to give engineered bacteria a similar line of defense against transposons and other selfish elements in their genomes. We demonstrate that this CRISPR interference against mobile elements (CRISPRi-ME) approach can be used to simultaneously repress two different transposon families in Escherichia coli, thereby increasing the evolutionary stability of costly protein expression. We further show that silencing a transposon in Acinetobacter baylyi ADP1 reduces mutation rates by a factor of 5, nearly as much as deleting all copies of this element from its genome. By deploying CRISPRi-ME on a broad-host-range vector, we have created a generalizable platform for stabilizing the genomes of engineered bacterial cells for applications in metabolic engineering and synthetic biology.

Keywords: genome stability; insertion sequence; reduced mutation cell; selfish DNA.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Acinetobacter / genetics*
  • CRISPR-Cas Systems
  • Clustered Regularly Interspaced Short Palindromic Repeats
  • DNA Transposable Elements / genetics
  • Escherichia coli / genetics*
  • Evolution, Molecular*
  • Genetic Vectors
  • Genome, Bacterial
  • Genomic Instability*
  • Metabolic Engineering / methods*
  • Mutation
  • Plasmids / genetics
  • RNA Interference
  • Repetitive Sequences, Nucleic Acid / genetics*
  • Synthetic Biology / methods*


  • DNA Transposable Elements

Supplementary concepts

  • Acinetobacter baylyi