Single Cell Variability of CRISPR-Cas Interference and Adaptation

Abstract

CRISPR-Cas defence is a combination of adaptation to new invaders by spacer acquisition, and interference by targeted nuclease activity. While these processes have been studied on a population level, the individual cellular variability has remained unknown. Here, using a microfluidic device combined with time-lapse microscopy, we monitor invader clearance in a population of Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we show large cell-to-cell variability of clearance times, which originates from primed CRISPR adaptation. Faster growth and cell division, as well as higher levels of Cascade, increase the chance of clearance by interference. In contrast, faster growth is associated with decreased chances of clearance by priming. A mathematical model explains the experimental findings, and identifies Cascade binding to the mutated invader DNA, rather than spacer integration, as the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond to invading threats in a timely manner. We conjecture that CRISPR-Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.

Investigating the relationship between CRISPR-Cas content and growth rate in bacteria

“…They found that spacer acquisition occurs predominantly during the late exponential/early stationary phase. In line with this study, McKenzie et al (2) observed that the E. coli cells that adapted and cleared the target DNA earlier grew significantly slower than the population means. The soil-dwelling bacterium Pseudomonas aeruginosa can also infect the plant and human bodies.…”

“…1 Correlation of spacer abundance with empirical MDT and optimal growth temperature. 2 Correlation of spacer abundance with predicted MDT and optimal growth temperature. MDT, minimal doubling time.…”

CRISPR memories in single cells

“…Brouns and coworkers take an important step to addressing this challenge by studying spacer acquisition and invader clearance at the single‐cell level (McKenzie et al , 2022). They focused on the type I‐E CRISPR‐Cas system in the bacterium Escherichia coli , which generally uses two modes of spacer acquisition called naive acquisition and primed acquisition (Fineran et al , 2014; Levy et al , 2015).…”