BPS2026 – DNA loop extrusion and obstacle bypass by the Wadjet SMC motor

Chromosomes fold into compact yet dynamic 3D structures through DNA loop extrusion (LE), driven by conserved ATP-powered structural maintenance of chromosomes (SMC) motors. SMC complexes form ring-shaped structures that entrap chromosomal DNA molecules. Loop-extruding SMC complexes encounter various obstacles on their chromosomal translocation tracks. Remarkably, they can efficiently bypass many of these obstacles, including those larger than the ring lumen, but the molecular mechanisms governing DNA translocation and obstacle bypass remain poorly understood. We use the bacterial Wadjet SMC complex as a model for biochemical, biophysical, and structural studies. Wadjet is an SMC-based bacterial defense system that restricts smaller circular DNA molecules (plasmids) through DNA cleavage. It comprises a canonical SMC sensor component (JetABC), related to the E. coli SMC complex MukBEF, and a nuclease effector (JetD). Based on structural data, we propose a DNA translocation mechanism involving repeated capture of DNA segments, enabling the SMC motor to make large steps along the DNA, explaining many observations made by single molecule imaging. Using a plasmid cleavage assay, we show that Wadjet can efficiently bypass very large obstacles when these are tethered to the extruded DNA by a single-stranded DNA (ssDNA) or RNA linker. This bypass is mediated by the selective and transient entrapment of the linker within a channel formed by the SMC hinge, which functions as an obligate gate—permitting ssDNA passage while excluding double-stranded DNA (dsDNA). Threading the linker through the hinge gate allows the obstacle to remain outside the SMC ring and follow a trajectory distinct from its associated dsDNA, which continues to be entrapped as it is extruded by the SMC motor. Together, our work presents the first molecular model that integrates stable dsDNA entrapment by the SMC motor with efficient bypassing of very large obstacles.