Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events

Abstract

The condensin SMC protein complex organizes chromosomal structure by extruding loops of DNA. Its ATP-dependent motor mechanism remains unclear but likely involves steps associated with large conformational changes within the ∼50 nm protein complex. Here, using high-resolution magnetic tweezers, we resolve single steps in the loop extrusion process by individual yeast condensins. The measured median step sizes range between 20–40 nm at forces of 1.0–0.2 pN, respectively, comparable with the holocomplex size. These large steps show that, strikingly, condensin typically reels in DNA in very sizeable amounts with ∼200 bp on average per single extrusion step at low force, and occasionally even much larger, exceeding 500 bp per step. Using Molecular Dynamics simulations, we demonstrate that this is due to the structural flexibility of the DNA polymer at these low forces. Using ATP-binding-impaired and ATP-hydrolysis-deficient mutants, we find that ATP binding is the primary step-generating stage underlying DNA loop extrusion. We discuss our findings in terms of a scrunching model where a stepwise DNA loop extrusion is generated by an ATP-binding-induced engagement of the hinge and the globular domain of the SMC complex.

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

“…Comparison between Figures 4D and 4H further highlight the equivalence of the two situations (i.e., fixed tension and end-to-end extension) for low DNA tension/extension. Recent observations of step size distributions for yeast condensin ( 54 ) are in good agreement with our results.…”

“…Figure 4F ). Recent observations of large ATP hydrolysis-independent contractions of SMCC-DNA complexes ( 54 ) are likely looking at the DNA segment capture process rather than protein conformational change.…”

“…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. Our model is unique in including the known topological interaction between the SMCC tripartite protein ring and DNA, which is key to maintaining the translocation in one direction along DNA observed experimentally ( 54 ).…”

“…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. Our model is unique in including the known topological interaction between the SMCC tripartite protein ring and DNA, which is key to maintaining the translocation in one direction along DNA observed experimentally ( 54 ). Our model also describes the ATP binding and hydrolysis cycle and associated structural transitions of the SMCC, again based on experimental structural data.…”

Can DyeCycling break the photobleaching limit in single-molecule FRET?

“…The central dogma of molecular biology -DNA is transcribed into RNA, RNA is translated into proteins -is rife with dynamic heterogeneity [89]. Pauses during RNA polymerase activity have been shown to be essential in regulating transcription and thus gene expression [90][91][92][93][94].…”