Structure-function relationships of SMC protein complexes for DNA loop extrusion

Rah

Janissen

et al. 2021

Nucleic Acids Research

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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.

Section: Discussionsupporting

confidence: 90%

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

Rah

Janissen

et al. 2021

Nucleic Acids Research

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“…Indeed, the I-to-folded state transition was suggested to be triggered by ATP hydrolysis (17,54). By contrast, our result that ATP binding is the step-generating process is in good agreement with cryo-EM results on cohesin (20,21,55,56) and with AFM data on condensin that showed a transition from an extended state to a hinge-engaged state upon ATP binding (18). In addition, our results are also consistent with recent AFM and single-molecule FRET study on human cohesin that showed that ATP-binding promotes head domain engagement that provides DNA binding sites via hingehead interaction (57).…”

Section: Atp Binding and Hydrolysis Relate To Two Distinct Mechanistic Processessupporting

confidence: 90%

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

Rah

Janissen

et al. 2020

Preprint

Self Cite

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 magnetic tweezers, we resolve single steps in loop extrusion by individual yeast condensins. Step sizes range between 20-45 nm at forces of 1.0-0.2 pN, respectively, comparable to the complex size. The large steps show that condensin reels in DNA in very sizeable amounts, up to ~600 bp per extrusion step, consistent with the non-stretched 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 the 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.

“…The cohesin-SMC complex is important for interphase chromosome organization [ 157 , 158 ], and in-vitro experiments have shown that the complex forms condensates via the BIPS mechanism [ 20 ]. Cohesin is a good model for a protein with multiple DNA-binding sites.…”

Section: Local Phase Separation Models: Bips and Sipsmentioning

confidence: 99%

“…Because it acts primarily as a motor protein to extrude a DNA loop for interphase chromosome organization, there are at least two DNA-binding sites on the surface of the cohesin protein for the relative motion of two different DNA-binding sites in an ATP hydrolysis-dependent manner. Multiple DNA-binding sites on the cohesin protein have been confirmed by various structural studies, suggesting that it can bridge distant DNA segments [ 158 , 159 , 160 , 161 ].…”

Section: Local Phase Separation Models: Bips and Sipsmentioning

confidence: 99%

Current Understanding of Molecular Phase Separation in Chromosomes

Hwang

Choi

2021

IJMS

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Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation. Recent studies have found that biomolecular phase separation is involved in a wide range of cellular processes. In particular, phase separation is involved in the formation and regulation of chromosome structures at various levels. Here, we review the current understanding of biomolecular phase separation related to chromosomes. First, we discuss the fundamental principles of phase separation and introduce several examples of nuclear/chromosomal biomolecular assemblies formed by phase separation. We also briefly explain the experimental and computational methods used to study phase separation in chromosomes. Finally, we discuss a recent phase separation model, termed bridging-induced phase separation (BIPS), which can explain the formation of local chromosome structures.