Single cell variability of CRISPR‐Cas interference and adaptation

While CRISPR-Cas defence mechanisms have been studied on a
population level, their temporal dynamics and variability in indi-
vidual cells have remained unknown. Using a microfluidic device,
time-lapse microscopy and mathematical modelling, we studied
invader clearance in Escherichia coli across multiple generations.
We observed that CRISPR interference is fast with a narrow distri-
bution of clearance times. In contrast, for invaders with escaping
PAM mutations we found large cell-to-cell variability, which origi-
nates from primed CRISPR adaptation. Faster growth and cell divi-
sion and higher levels of Cascade increase the chance of clearance
by interference, while slower growth is associated with increased
chances of clearance by priming. Our findings suggest that Cas-
cade binding to the mutated invader DNA, rather than spacer inte-
gration, is the main source of priming heterogeneity. The highly
stochastic nature of primed CRISPR adaptation implies that only
subpopulations of bacteria are able to respond quickly to invading
threats. We conjecture that CRISPR-Cas dynamics and heterogene-
ity at the cellular level are crucial to understanding the strategy of
bacteria in their competition with other species and phages.