Ref HAL: hal-01931248_v1
Exporter : BibTex | endNote
Résumé:

Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a non-linear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and travelling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.

Ref HAL: hal-01931233_v1
Exporter : BibTex | endNote
Résumé:

Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a non-linear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and travelling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.

Ref HAL: hal-01881265_v1
Exporter : BibTex | endNote
Résumé:

Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component, fueled by adenosine triphosphate machinery called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simplelinear reaction-diffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation and subsequent symmetricalpositioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a non-linear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and travelling wave regimes triggered by the dynamical spontaneous breaking ofrotational symmetry.

Ref HAL: hal-01561696_v1
Ref Arxiv: 1707.01373
DOI: 10.1088/1367-2630/aaad39
WoS: 000428767700002
Ref. & Cit.: NASA ADS
Exporter : BibTex | endNote
4 Citations
Résumé:

The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. With this approach we consider the genomic organization of such a protein-DNA cluster around a single high-affinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate (parS) binding site.

Commentaires: 14 pages, 7 figures

Ref HAL: hal-01493264_v1
Ref Arxiv: 1702.06804
DOI: 10.1039/c7sm00395a
WoS: 000400876600012
Ref. & Cit.: NASA ADS
Exporter : BibTex | endNote
6 Citations
Résumé:

We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary parts which can bind to each other. At the critical temperature, the (un)zipping is unbiased and the two strands open and close as a zipper. The number of closed base pairs $n(t)$ displays a subdiffusive motion characterized by a variance growing as $\langle \Delta n^2(t) \rangle \sim t^\alpha$ with $\alpha < 1$ at long times. Our theory provides an estimate of both the asymptotic anomalous exponent $\alpha$ and of the subleading correction term, which are both in excellent agreement with numerical simulations. The results indicate that the tension propagation theory captures the relevant features of the dynamics and shed some new insights on related polymer problems characterized by anomalous dynamical behavior.

Commentaires: 8 pages, 3 figures, submitted

Ref HAL: hal-01493262_v1
Ref Arxiv: 1702.07372
DOI: 10.1103/PhysRevLett.119.028101
WoS: 000405367800016
Ref. & Cit.: NASA ADS
Exporter : BibTex | endNote
14 Citations
Résumé:

Efficient bacterial chromosome segregation typically requires the coordinated action of a three-component machinery, fueled by adenosine triphosphate, called the partition complex. We present a phenomenological model accounting for the dynamic activity of this system that is also relevant for the physics of catalytic particles in active environments. The model is obtained by coupling simple linear reaction-diffusion equations with a proteophoresis, or “volumetric” chemophoresis, force field that arises from protein-protein interactions and provides a physically viable mechanism for complex translocation. This minimal description captures most known experimental observations: dynamic oscillations of complex components, complex separation, and subsequent symmetrical positioning. The predictions of our model are in phenomenological agreement with and provide substantial insight into recent experiments. From a nonlinear physics view point, this system explores the active separation of matter at micrometric scales with a dynamical instability between static positioning and traveling wave regimes triggered by the dynamical spontaneous breaking of rotational symmetry.

Commentaires: 6 pages, 3 figures

Ref HAL: hal-01950249_v1
Exporter : BibTex | endNote
Résumé:

Bacteria, a few μm in length, have the feature to store the genome in a subvolume of the cell without membrane. The bacterial cell cycle relies on a series of essential processes such as DNA replication, transcription and segregation. The mechanisms driving segregation of the genome are still unclear, mainly because the processes overlap in time and take place in the same cellular compartment. The active ParABS partition system is the only type known on chromosomes and is prevalent on low-copy number plasmids,namely the F-plasmid involved in bacterial resistance to antibiotics. ParABS is composed of three components: the proteins ParA and ParB, respectively a molecular motor (ATPase) and a binding protein, and parS, a sequence of specific binding sites. We describe the organization and architecture of the partition complex. Our model is supported by experimental data from ChIP-sequencing (LMGM, Toulouse) and super resolution microscopy techniques (CBS, Montpellier).