Persisters are primed for CRISPR-Cas adaptation

Abstract

In the evolutionary battle between bacteria and mobile genetic elements, such as bacteriophage viruses and plasmids, bacteria have developed intricate defense systems. Among these, the CRISPR-Cas system has been extensively studied and harnessed as a revolutionary gene editing tool. However, while the biochemical process by which this microbial immune system acquires genetic CRISPR memory and immunity against invaders has been comprehensively examined, fundamental questions about the bacterial physiological state underlying how and when CRISPR memory is formed have only been partially explored. Naive CRISPR adaptation is generally rare, but occurs more frequently when bacteria are challenged with replication-deficient phages. In such scenarios, bacteria are not under immediate threat and have ample time to adapt to the phage DNA, without risking cell death. Accordingly, slow growth caused by low temperatures, low aeration, or bacteriostatic antibiotics promotes CRISPR adaptation, possibly by allowing the Cas complexes more time to adapt before being outpaced. Persister cells are dormant antibiotic-tolerant subpopulations of cells with limited metabolic activity. When a mobile genetic element invades a persister cell, its replication is halted until the host cell resumes growth, providing an ideal opportunity for CRISPR adaptation. Here, we show that transiently dormant Escherichia coli persister cells acquire CRISPR immunity 10-fold more frequently than the general bacterial population. Thus, persister cells, in addition to being notoriously antibiotic tolerant, are primed for CRISPR-Cas adaptation and may be in a state of heightened immune capacity and evolution, securing the survival of the population.