Restriction endonuclease cleavage of phage DNA enables resuscitation from Cas13-induced bacterial dormancy

Toxin/Antitoxin Systems Induce Persistence and Work in Concert with Restriction/Modification Systems to Inhibit Phage

“…Along with the formation of persister cells, some cells indubitably succumb to phage attack; however, our results indicate the primary purpose of the anti-phage systems is not what has been termed ‘abortive infection’ in which the phage inhibition system kills the cells 29, 45, but instead, these systems protect the cells and allow them to survive phage attack. Similar results showing dormancy have been seen with type VI CRISPR-Cas and restriction/modification systems 47 .…”

“…Hence, our results suggest toxin/antitoxin systems act first to reduce metabolism, followed by restriction/modification systems, to undermine phage attack. Similarly, CRISPR-Cas has been shown to act first, followed by restriction/modification systems in Listeria spp 47 . Our results showing synergy between toxin/antitoxin and restriction/modification systems are significant since both of these phage defense systems are found in nearly all bacteria (unlike many other phage inhibition systems such as CRISPR-Cas, CBASS and retrons that are found in 39%, 13% and 11% of procaryote genomes, respectively 43 ), which suggests this interaction is widespread and may be dominant for phage inhibition.…”

“…This general concept of allowing back-up DNA-targeting enzymes to function while the cell is dormant has been proposed for the type III/VI CRISPR-Cas systems 30, 44 and demonstrated while this work was being prepared for type VI CRISPR-Cas in Listeria spp. 47 ; however, the benefit of dormancy has not been suggested for the plethora of recently-discovered, non-CRSPR-Cas phage inhibition systems. Here we demonstrate that (i) dormancy in the form of persistence is a key aspect of phage inhibition of non-CRISPR-Cas systems and that (ii) restriction/modification is utilized during the dormant state.…”

Accumulation of defense systems in phage-resistant strains of Pseudomonas aeruginosa

“…Our findings demonstrate the significance of the individual defense systems in predicting the susceptibility of P. aeruginosa strains to phages. However, factors such as genetic context, interactions among defense systems (49,(51)(52)(53), the presence of unknown defense systems, and anti-defense mechanisms will affect the final outcome of phage infection. Further research is required to enhance the predictive accuracy of genomic analysis, which could prove beneficial for ecological and evolutionary studies.…”

“…We expect that these combinations of defense systems could provide a broader range of phage protection through the complementary phage specificities of each individual defense system. The complementary activities of naturally co-occurring defense systems have also been found to enable resuscitation from defense system-induced bacterial dormancy (RM and CRISPR-Cas) ( 49 ) and to prevent plasmid dissemination in V. cholerae El Tor strains (DdmABC and DdmDE) ( 50 ), the latter proposing that defense system cooperation might play a role in bacterial pathogenicity.…”