Hysteresis in DNA compaction by Dps is described by an Ising model
| Autor: | Nynke H. Dekker, Anne S. Meyer, Elio A. Abbondanzieri, David Dulin, M.W. Docter, Natalia N. Vtyurina |
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| Rok vydání: | 2016 |
| Předmět: |
DNA
Bacterial 0301 basic medicine genetic structures Cooperativity 030106 microbiology Biology DNA condensation Dissociation (chemistry) 03 medical and health sciences chemistry.chemical_compound Bacterial Proteins Ising model Fluorescence microscope Molecule Magnesium Multidisciplinary Hysteresis Circular bacterial chromosome Biological Sciences Hydrogen-Ion Concentration Models Theoretical DNA-Binding Proteins Crystallography 030104 developmental biology chemistry Biophysics Salts Dps DNA |
| Zdroj: | Proceedings of the National Academy of Sciences of the United States of America, 113(18) |
| ISSN: | 1091-6490 0027-8424 |
| Popis: | In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps-DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps. Real-time in vitro studies demonstrated a highly cooperative process of Dps binding characterized by an abrupt collapse of the DNA extension, even under applied tension. Surprisingly, we also discovered a reproducible hysteresis in the process of compaction and decompaction of the Dps-DNA complex. This hysteresis is extremely stable over hour-long timescales despite the rapid binding and dissociation rates of Dps. A modified Ising model is successfully applied to fit these kinetic features. We find that long-lived hysteresis arises naturally as a consequence of protein cooperativity in large complexes and provides a useful mechanism for cells to adopt unique epigenetic states. |
| Databáze: | OpenAIRE |
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