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

Abstract

Structural maintenance of chromosomes (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 transiently in two separate chambers. Single-molecule imaging and cryo–electron microscopy suggest a putative power-stroke movement at the first chamber that feeds DNA into the SMC–kleisin ring upon adenosine triphosphate binding, whereas 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 SMC reaction cycle determines the directionality of DNA loop extrusion.

Can pseudotopological models for SMC-driven DNA loop extrusion explain the traversal of physical roadblocks bigger than the SMC ring size?

“…According to the models of Shaltiel et al 12 and Nomidis et al 13 , SMC complexes entrap DNA pseudotopologically, i.e., the two DNA strands that form the base of a loop pass through the ring structure formed by the SMC and kleisin subunits of these complexes. In view of the clear observation of the passage of roadblocks bigger than the SMC ring size into extruded loops in our experiments, the authors of these papers attempted to explain our observations within the context of their models.…”

“…After these data appeared on bioRxiv in July 2021 11 , two new pseudotopological models were proposed by Shaltiel et al ("hold-and-feed mechanism" 12 ) and by Nomidis et al ("segment-capture model" 13 ). In the light of the roadblock experiments, the authors of these models attempted to explain the passage of the huge roadblocks within the context of their models.…”

Making Mitotic Chromosomes in a Test Tube

“…It is thus believed that the positive supercoil introducing activity of condensin I is physiologically relevant. Conversely, increasing lines of evidence show that condensins are capable of extruding DNA loops in an ATP hydrolysis-dependent manner [ 63 , 69 , 70 , 71 , 72 , 73 ] ( Figure 5 A). Loop extrusion by condensins has been observed not only in an experimental setup made of purified proteins but also in a mitotic egg extract [ 74 ].…”

Characterization of the NSE6 subunit of thePhyscomitrium patensPpSMC5/6 complex

“…In prokaryotic SMC and eukaryotic SMC5/6 complexes, kleisins interact with KITE (Kleisin-Interacting Tandem winged-helix Element) subunits (Palecek & Gruber, 2015), while cohesin and condensin complexes contain HAWK (HEAT-Associated With Kleisin) subunits (Wells et al , 2017). The SMC head-kleisin-KITE (or HAWK) form a compartment which anchors DNA during loop extrusion (Shaltiel et al , 2022; Yu et al , 2022). Uniquely, in addition to core SMC-kleisin-KITE subunits (called SMC5/SMC6-NSE4-NSE1/NSE3), SMC5/6 complexes contain highly conserved essential NSE2 SUMO-ligases (Andrews et al , 2005; Zhao & Blobel, 2005) which bind to SMC5 arms (Duan et al , 2009).…”

“…In prokaryotic SMC and eukaryotic SMC5/6 complexes, kleisins interact with KITE (Kleisin-Interacting Tandem winged-helix Element) subunits (Palecek & Gruber, 2015), while cohesin and condensin complexes contain HAWK (HEAT-Associated With Kleisin) subunits (Wells et al, 2017). The SMC head-kleisin-KITE (or HAWK) form a compartment which anchors DNA during loop extrusion (Shaltiel et al, 2022;Yu et al, 2022).…”