The SMC Hinge is a Selective Gate for Obstacle Bypass

Abstract

DNA loop-extruding SMC complexes play vital roles in genome maintenance and DNA immunity. However, the ability of these ring-shaped DNA motors to navigate large DNA-bound obstacles, such as DNA/RNA polymerases and ribosomes in prokaryotes, has remained unclear. Here, we demonstrate that a bacterial SMC Wadjet complex can efficiently bypass obstacles larger than the SMC coiled coil lumen if they are linked to the extruded DNA by single-stranded DNA (ssDNA). This process is mediated by the selective entrapment of the ssDNA linker within the SMC hinge channel, which acts as an obligate gate--permitting ssDNA passage while excluding double-stranded DNA (dsDNA). By threading the linker through the hinge gate as dsDNA is translocated through the SMC motor, the obstacle can follow a trajectory distinct from its associated dsDNA, remaining outside the SMC ring. This mechanism enables continuous dsDNA entrapment while successfully bypassing obstacles. We show that hinges of diverse SMC complexes including eukaryotic condensin and Smc5/6 also selectively accommodate ssDNA, suggesting that hinge bypass is a conserved feature across SMC proteins. We demonstrate that while the hinge domain is essential for obstacle bypass, it is dispensable for loop extrusion, showing that these functions are independent, provided by separate SMC modules. These findings uncover the long-sought function of the SMC hinge toroid and provide the first mechanistic explanation for how DNA-entrapping SMC complexes can extrude loops on chromosomal DNA densely populated with obstacles. Integrating hinge bypass into the DNA loop extrusion model, we propose that the hinge may also facilitate the passage of RNA and peptide, enabling bypass of transcription-associated ribonucleoprotein complexes and other SMC complexes.