DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage

Structural maintenance of chromosomes (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA. Here, we show that JetABCD restricts circular plasmids with an upper size limit of about 100 kb, while a linear plasmid evades restriction. Purified JetABCD complexes cleave circular DNA molecules regardless of DNA helical topology; cleavage is DNA sequence-nonspecific and depends on the SMC ATPase. A cryo-EM structure reveals a distinct JetABC dimer-of-dimers geometry with the two SMC dimers facing in opposite direction—rather than the same as observed with MukBEF. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and propose the ‘total extrusion model’ for DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a JetABCD complex. Total extrusion cannot be achieved on the larger chromosome, explaining how self-DNA may evade processing.