Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events
| Autor: | Jacob W. J. Kerssemakers, Sang-Hyun Rah, Richard Janissen, Je-Kyung Ryu, Davide Michieletto, Cees Dekker, Andrea Bonato |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2022 |
| Předmět: |
Magnetic tweezers
Saccharomyces cerevisiae Proteins Base pair AcademicSubjects/SCI00010 Condensin Mutant Saccharomyces cerevisiae 03 medical and health sciences Molecular dynamics chemistry.chemical_compound 0302 clinical medicine Genetics DNA Fungal 030304 developmental biology Adenosine Triphosphatases 0303 health sciences biology Chemistry SMC protein Gene regulation Chromatin and Epigenetics Chromatin DNA-Binding Proteins Multiprotein Complexes Biophysics biology.protein Nucleic Acid Conformation Extrusion 030217 neurology & neurosurgery DNA Protein Binding |
| Zdroj: | Ryu, J-K, Rah, S-H, Janissen, R, Kerssemakers, J W J, Bonato, A, Michieletto, D & Dekker, C 2022, ' Condensin extrudes DNA loops in steps up to hundreds of base pairs that are generated by ATP binding events ', Nucleic Acids Research, vol. 50, no. 2, pp. 820-832 . https://doi.org/10.1093/nar/gkab1268 Nucleic acids research, 50(2) Nucleic Acids Research bioRxiv Nucl. Acid Res. 50 |
| DOI: | 10.1093/nar/gkab1268 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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