Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage

SMCs are essential protein complexes highly conserved in all life kingdoms. SMCs fold chromosomal DNA into large loops by means of an extrusion mechanism that remains mysterious. The DNA topology Lab of IBMB has uncovered how Condensin, a eukaryotic SMC, grabs and deforms the DNA to produce the translocation steps required to enlarge the extruding loops. They propose a “pinch and merge” mechanism of action.

Abstract

Condensin, an SMC (structural maintenance of chromosomes) protein complex, extrudes DNA loops using an ATP-dependent mechanism that remains to be elucidated. Here, we show how condensin activity alters the topology of the interacting DNA. High condensin concentrations restrain positive DNA supercoils. However, in experimental conditions of DNA loop extrusion, condensin restrains negative supercoils. Namely, following ATP-mediated loading onto DNA, each condensin complex constrains a DNA linking number difference (∆Lk) of −0.4. This ∆Lk increases to −0.8 during ATP binding and resets to −0.4 upon ATP hydrolysis. These changes in DNA topology do not involve DNA unwinding, do not spread outside the condensin-DNA complex and can occur in the absence of the condensin subunit Ycg1. These findings indicate that during ATP binding, a short DNA domain delimited by condensin is pinched into a negatively supercoiled loop. We propose that this loop is the feeding segment of DNA that is subsequently merged to enlarge an extruding loop. Such a “pinch and merge” mechanism implies that two DNA-binding sites produce the feeding loop, while a third site, plausibly involving Ycg1, might anchor the extruding loop.

Reference:

Belén Martínez-García*; Sílvia Dyson*; Joana Segura*; Alba Ayats; Erin E Cutts; Pilar Gutierrez-Escribano; Luís Aragón; Joaquim Roca*. Condensin pinches a short negatively supercoiled DNA loop during each round of ATP usage. The EMBO Journal. 19 Dec (2022), e111913. doi: 10.15252/embj.2022111913