A hold-and-feed mechanism drives directional DNA loop extrusion by condensin

Abstract

SMC protein complexes structure genomes by extruding DNA loops, but the molecular mechanism that underlies their activity has remained unknown. We show that the active condensin complex entraps the bases of a DNA loop in two separate chambers. Single-molecule and cryo-electron microscopy provide evidence for a power-stroke movement at the first chamber that feeds DNA into the SMC-kleisin ring upon ATP binding, while the second chamber holds on upstream of the same DNA double helix. Unlocking the strict separation of ‘motor’ and ‘anchor’ chambers turns condensin from a one-sided into a bidirectional DNA loop extruder. We conclude that the orientation of two topologically bound DNA segments during the course of the SMC reaction cycle determines the directionality of DNA loop extrusion.

DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations

“…As long as DNA remains tethered in the interior of the SMC-kleisin ring, this mechanism generates one-sided, asymmetric loop extrusion, similar to the external safety belt. Recent DNA mapping studies suggest that condensin may bind DNA in this manner (66).…”

“…2B) is attached to the exterior of the kleisin subunit, as is thought to be accomplished by the “safety belt” of yeast condensin. This DNA binding site is formed by Ycg1 and part of Brn1 (31), distinct from the regions of the Brn1 and Ycs4 involved in the ATP-driven angular conformational change observed in cryo-EM experiments (20, 66). Combining safety-belt site binding with the threading of DNA through the lower compartment leads to formation of a DNA loop.…”

“…In addition to being supported by experimental observations of topological linkage of SMCCs to DNA mentioned above, this topological feature is key to the high degree of processivity and conserved translocation directionality of SMCCs along their left-right symmetric dsDNA substrate observed experimentally (35). Without this linkage, SMCCs would be unable to preserve their direction of translocation along dsDNA (41, 66). We also emphasize that in this model the SMCC transitions are decoupled from DNA motion, in the sense that steps in the protein conformational cycle are not contingent on e.g.…”

“…The key insight of Ref. (66) is that in this obstacle-blocked state, DNA on the upstream side of the obstacle (Fig. S6, green DNA) can still be captured by the SMCC leading to extrusion of a loop with the obstacle effectively acting as the "loop anchor" (Fig.…”

Inter- and intra-Subunit interactions driving the MukBEF ATPase

“…Yeast condensin extrudes DNA loops in a unidirectional manner (12,13), whereas human cohesion extrudes loops bidirectionally (14,15). A “hold and feed” mechanism for loop extrusion has recently been proposed (16). Whereas a similar activity for MukBEF has not yet been reported, it has been shown that the protein complex organizes the E. coli chromosome into an axial core from which loops of DNA protrude (17).…”