Folding of cohesin’s coiled coil is important for Scc2/4-induced association with chromosomes

Abstract

Cohesin’s association with and translocation along chromosomal DNAs depend on an ATP hydrolysis cycle driving the association and subsequent release of DNA. This involves DNA being ‘clamped’ by Scc2 and ATP-dependent engagement of cohesin’s Smc1 and Smc3 head domains. Scc2’s replacement by Pds5 abrogates cohesin’s ATPase and has an important role in halting DNA loop extrusion. The ATPase domains of all SMC proteins are separated from their hinge dimerisation domains by 50-nm-long coiled coils, which have been observed to zip up along their entire length and fold around an elbow, thereby greatly shortening the distance between hinges and ATPase heads. Whether folding exists in vivo or has any physiological importance is not known. We present here a cryo-EM structure of the apo form of cohesin that reveals the structure of folded and zipped-up coils in unprecedented detail and shows that Scc2 can associate with Smc1’s ATPase head even when it is fully disengaged from that of Smc3. Using cysteine-specific crosslinking, we show that cohesin’s coiled coils are frequently folded in vivo, including when cohesin holds sister chromatids together. Moreover, we describe a mutation (SMC1D588Y) within Smc1’s hinge that alters how Scc2 and Pds5 interact with Smc1’s hinge and that enables Scc2 to support loading in the absence of its normal partner Scc4. The mutant phenotype of loading without Scc4 is only explicable if loading depends on an association between Scc2/4 and cohesin’s hinge, which in turn requires coiled coil folding.

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

“…These conformational changes are supported by ultrastructural experimental data. Angular conformational changes of the lower compartment region of similar symmetry to those in our model and associated with ATP binding have been observed in cryo-EM studies of condensin and cohesin ( 20 , 27 , 28 , 53 , 66 ). In the case of yeast condensin this angular change involves the kleisin Brn1 and the Ycs4 HEAT-repeat subunit, and not the Ycg1 HEAT-repeat subunit ( 20 , 67 ).…”

“…The positions of the elbow in condensin, cohesin and MukBEF are different, with hinge meeting arms, joints and heads, respectively, in those complexes, and the structure of the elbow is not conserved. This suggests elbow bending being a feature arising from divergent evolution, rather than being a feature fundamental to translocation and loop extrusion ( 20 , 26 , 53 ). While other simulation models can reproduce aspects of the experimental data ( 46 , 54 ), they are more coarse-grained than the model of the present paper.…”

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

“…These conformational changes are supported by ultrastructural experimental data. Angular conformational changes of the lower compartment region of similar symmetry to those in our model and associated with ATP binding have been observed in cryo-EM studies of condensin and cohesin (20,26,28,52,65). In the case of yeast condensin this angular change involves the kleisin Brn1 and the Ycs4 HEAT-repeat subunit, and not the Ycg1 HEATrepeat subunit (20,66).…”

“…The positions of the elbow in condensin, cohesin and MukBEF are different, with hinge meeting arms, joints and heads, respectively, in those complexes, and the structure of the elbow is not conserved. This suggests elbow bending being a feature arising from divergent evolution, rather than being a feature fundamental to translocation and loop extrusion (20, 27, 52). We also note that scrunching and other SMCC-walking-based models (49) have difficulty generating steps along DNA that are larger than the complex itself, as has been observed for SMCCs (53); in contrast steps larger than the SMCC itself occur naturally in models that are based on DNA loop capture (41, 45).…”

Cohesin mediates DNA loop extrusion by a “swing and clamp” mechanism

“…These results confirm the asymmetric bending seen by HS-AFM, show that the hinge bends toward the head of SMC3, and indicate that the hinge and the SMC3 head come into close proximity of up to ∼4 nm. As mentioned, this distance is shorter than the head-hinge distance observed by cryo-EM ( Shi et al., 2020 ; Petela et al., 2021 ), indicating that the hinge can come closer to the SMC3 head than can be seen in these cryo-EM structures.…”