Oligomerization and ATP stimulate condensin-mediated DNA compaction

Abstract

Large-scale chromatin remodeling during mitosis is catalyzed by a heteropentameric enzyme known as condensin. The DNA-organizing mechanism of condensin depends on the energy of ATP hydrolysis but how this activity specifically promotes proper compaction and segregation of chromosomes during mitosis remains poorly understood. Purification of budding yeast condensin reveals that it occurs not only in the classical heteropentameric “monomer” form, but that it also adopts much larger configurations consistent with oligomerization. We use a single-DNA magnetic tweezers assay to study compaction of DNA by yeast condensin, with the result that only the multimer shows ATP-enhanced DNA-compaction. The compaction reaction involves step-like events of 200 nm (600 bp) size and is strongly suppressed by forces above 1 pN, consistent with a loop-capture mechanism for initial binding and compaction. The compaction reactions are largely insensitive to DNA torsional stress. Our results suggest a physiological role for oligomerized condensin in driving gradual chromatin compaction by step-like and slow “creeping” dynamics consistent with a loop-extrusion mechanism.

Chromosome organization by one-sided and two-sided loop extrusion

“…In our model, switches occur at rate k switch ; by switching, inactive subunits become active and vice versa. Thus, LEF subunits have trajectories similar to the one shown in Figure 1 Although not yet observed experimentally, we hypothesize that switching activity of SMC complexes could potentially be induced by exchange of subunits within the SMC complex, different solution conditions, or post-translational or genetic modifications, all of which can alter SMC complex behavior in experiments Elbatsh et al, 2019;Ganji et al, 2018;Keenholtz et al, 2017;Kleine Borgmann et al, 2013;Kschonsak et al, 2017) .…”

“…SMC complex oligomerization could facilitate chromosome organization by suppressing gap formation and/or promoting symmetric extrusion in various scenarios. In eukaryotes, in situ amino acid crosslinking (Barysz et al, 2015) and in vitro gel filtration (Keenholtz et al, 2017) suggest that condensins can oligomerize. Several experiments similarly suggest that cohesin may form oligomeric complexes in vivo (Cattoglio et al, 2019;Eng et al, 2015;Zhang et al, 2008) .…”

Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures

“…Loop extrusion has emerged as a vital mechanism underlying organization of chromosomes. SMC complexes (cohesin and condesnsins) can exert pN forces and are the prime candidates for driving the loop extrusion activity [26,27,[61][62][63][64]. In our model, extrusion of loops generates interloop repulsion that stretches the backbone; thus, loop extrusion may effectively control n, m, and α to drive chromosome compaction, and consequently, disentanglement in presence of Topo II.…”

Condensins and cohesins – one of these things is not like the other!

“…Integration of condensin structure and translocation properties into a coherent model becomes further complicated by step-size analyses. To address this point, experiments were performed where one end of a DNA molecule was tethered to a glass substrate, whereas the other end, which was attached to a streptavidin-coated magnetic bead, was kept under low-level tension (Keenholtz, et al, 2017). Upon addition of condensin and ATP, the DNA fiber quickly compacted, but analysis of bead migration (indicative of DNA compaction) revealed step sizes that were approximately four times the length of the 50 nm condensin complex (Keenholtz et al, 2017).…”