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

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.