About: Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome
Creator	Joyeux, Marc Junier, Ivan
Source	ArXiv
abstract	Bacterial genomes have been shown to be partitioned into several kilobases long chromosomal domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbors. Both in vivo and in vitro experiments have been performed to question the nature of the topological barriers at play, leading to several predictions on possible molecular actors. Here, we address the question of topological barriers using polymer models of supercoiled DNA chains. More specifically, we determine under which conditions DNA-bridging proteins may act as topological barriers. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. As a result, we find that DNA-bridging proteins must exert rather strong constraints on their binding sites: they must block the diffusion of the excess of twist through the two binding sites on the DNA molecule and, simultaneously, prevent the rotation of one DNA segment relative to the other one. Importantly, not all DNA-bridging proteins satisfy this second condition. For example, single bridges formed by proteins that bind DNA non-specifically, like H-NS dimers, are expected to fail with this respect. Our findings might also explain, in the case of specific DNA-bridging proteins like LacI, why multiple bridges are required to create stable independent topological domains. Strikingly, when the relative rotation of the DNA segments is not prevented, relaxation results in complex intrication of the two domains. Moreover, while the value of the torsional stress in each domain may vary, their differential is preserved. Our work also predicts that nucleoid associated proteins known to wrap DNA must form higher protein-DNA complexes to efficiently work as topological barriers.
has issue date	2020-08-13(xsd:dateTime)
has license	arxiv
sha1sum (hex)	14621ef5c1260421a70414e306f6b99eb8888f36
resource representing a document's title	Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome
resource representing a document's body	covid:14621ef5c1260421a70414e306f6b99eb8888f36#body_text
is schema:about of	named entity 'bacterial DNA' named entity 'nucleoid' named entity 'high affinity' named entity 'electrostatic interactions' named entity 'LacI' named entity 'conformation' named entity 'cell membrane' named entity 'cross-linking' named entity 'dimers' named entity 'binding sites' named entity 'circular DNA' named entity 'H-NS' named entity 'conformation' named entity 'conformation' named entity 'RNAP' named entity 'genomes' named entity 'torsional rigidity' named entity 'binding sites' named entity 'macromolecule' named entity 'circular DNA' named entity 'bacterial chromosome' named entity 'double-stranded DNA' named entity 'diffusion' named entity 'nucleoid' named entity 'writhe' named entity 'interact' named entity 'double-stranded DNA' named entity 'torsional energy' named entity 'macromolecule' named entity 'binding sites' named entity 'α, β' named entity 'binding sites' named entity 'linking number' named entity 'RNAP' named entity 'conformation' named entity '10 nm' named entity 'supercoiled' named entity 'molecular geometries' named entity 'RNAP' named entity 'topoisomerases' named entity 'circular DNA' named entity 'potential energy' named entity 'topology' named entity 'bacterial DNA' named entity 'LacI' named entity 'DNA supercoiling' named entity 'writhe' named entity 'diffusion' named entity 'plasmids' named entity 'cations' named entity 'writhe' named entity 'α and β' named entity 'genomic DNA' named entity 'plasmid' named entity 'supercoiling' named entity 'α and β' named entity 'S17' named entity 'DNA-binding protein' named entity 'RNAP' named entity 'molecule' named entity 'supercoils' named entity 'writhe' named entity 'diffusion' named entity 'α and β' named entity 'diffusion' named entity 'diffusion' named entity 'negative supercoils' named entity 'Escherichia coli' named entity 'plasmids' named entity 'recognition site' named entity 'monovalent' named entity 'overdamped' named entity 'duplexes' named entity 'electron' named entity 'repressor' named entity 'conformations' named entity 'α and β' named entity 'nicking enzyme' named entity 'tandem copies' named entity 'α and β' named entity 'diffusion' named entity 'chromosome' named entity 'DNA-binding domains' named entity 'diffusion' named entity 'cross-linking' named entity 'RNAP'

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