RESUMEN
The gram-negative bacterium Caulobacter crescentus is a powerful model organism for studies of bacterial cell cycle regulation. Although the major regulators and their connections in Caulobacter have been identified, it still is a challenge to properly understand the dynamics of its circuitry which accounts for both cell cycle progression and arrest. We show that the key decision module in Caulobacter is built from a limit cycle oscillator which controls the DNA replication program. The effect of an induced cell cycle arrest is demonstrated to be a key feature to classify the underlying dynamics.
Asunto(s)
Caulobacter crescentus/fisiología , Modelos Biológicos , Caulobacter crescentus/genética , Ciclo Celular/genética , División Celular , Replicación del ADNRESUMEN
An extended theoretical study of interface potentials in adsorbed colloid-polymer mixtures is performed. To describe the colloid-polymer mixture near a hard wall, a simple Cahn-Nakanishi-Fisher free-energy functional is used. The bulk phase behaviour and the substrate-adsorbate interaction are modelled by the free-volume theory for ideal polymers with polymer-to-colloid size ratios q = 0.6 and q = 1. The interface potentials are constructed with help from a Fisher-Jin crossing constraint. By manipulating the crossing density, a complete interface potential can be obtained from natural, single-crossing, profiles. The line tension in the partial wetting regime and the boundary tension along prewetting are computed from the interface potentials. The line tensions are of either sign, and descending with increasing contact angle. The line tension takes a positive value of 10(-14)-10(-12) N near a first-order wetting transition, passes through zero and decreases to minus 10(-14)-10(-12) N away from the first-order transition. The calculations of the boundary tension along prewetting yield values increasing from zero at the prewetting critical point up to the value of the line tension at first-order wetting.
RESUMEN
Recent experiments have demonstrated that the ATP-utilizing chromatin assembly and remodeling factor (ACF) is a dimeric, processive motor complex which can move a nucleosome more efficiently towards longer flanking DNA than towards shorter flanking DNA strands, thereby centering an initially ill-positioned nucleosome on DNA substrates. We give a Fokker-Planck description for the repositioning process driven by transitions between internal chemical states of the remodelers. In the chemical states of ATP hydrolysis during which the repositioning takes place a power stroke is considered. The slope of the effective driving potential is directly related to ATP hydrolysis and leads to the unidirectional motion of the nucleosome-remodeler complex along the DNA strand. The Einstein force relation allows us to deduce the ATP-concentration dependence of the diffusion constant of the nucleosome-remodeler complex. We have employed our model to study the efficiency of positioning of nucleosomes as a function of the ATP sampling rate between the two motors which shows that the synchronization between the motors is crucial for the remodeling mechanism to work.
Asunto(s)
Ensamble y Desensamble de Cromatina , Dimerización , Modelos Biológicos , Nucleosomas/genética , Nucleosomas/metabolismo , Adenosina Trifosfato/metabolismo , ProbabilidadRESUMEN
The stochastic dynamics of gene expression is often described by highly abstract models involving only the key molecular actors DNA, RNA, and protein, neglecting all further details of the transcription and translation processes. One example of such models is the "gene gate model," which contains a minimal set of actors and kinetic parameters, which allows us to describe the regulation of a gene by both repression and activation. Based on this approach, we formulate a master equation for the case of a single gene regulated by its own product-a transcription factor-and solve it exactly. The obtained gene product distributions display features of mono- and bimodality, depending on the choice of parameters. We discuss our model in the perspective of other models in the literature.
Asunto(s)
Regulación de la Expresión Génica , Modelos Genéticos , Procesos EstocásticosRESUMEN
Chromatin remodeling plays a crucial role in the activation or repression of transcription of eukaryotic genes. The chromatin remodeler ACF acts as a dimeric, processive motor to evenly space nucleosomes, favoring repression of gene transcription. Single-molecule experiments have established that ACF moves the nucleosome more efficiently towards the longer flanking DNA than towards the shorter flanking DNA, thereby centering an initially ill-positioned nucleosome on DNA substrates. In this paper we present a one-motor model with nucleosomal repositioning rates dependent on the DNA flanking length. The corresponding master equation is solved analytically with experimentally relevant parameter values. The velocity profile and the effective diffusion constant for nucleosome sliding, computed from the probability distributions, are in accordance with available experimental data. In order to address the observed kinetic pauses in experimental Förster Resonance Energy Transfer profiles, we extend the master equation to account for transitions between explicit motor states, i.e., adenosine triphosphate (ATP) loading and ATP hydrolysis in both ACF motors. The results of this extended two-motor model are compared to the previous effective one-motor model and allow insights into the role of the synchronization of the two motors acting on the nucleosome.
Asunto(s)
Modelos Químicos , Modelos Genéticos , Modelos Estadísticos , Proteínas Motoras Moleculares/química , Proteínas Motoras Moleculares/ultraestructura , Nucleosomas/química , Nucleosomas/ultraestructura , Simulación por Computador , Modelos Moleculares , Proteínas Motoras Moleculares/genética , Nucleosomas/genética , Procesos EstocásticosRESUMEN
We perform a theoretical study of the three-phase contact line and the line tension in an adsorbed colloid-polymer mixture near a first-order wetting transition, employing an interface displacement model. We use a simple free-energy functional to describe a colloid-polymer mixture near a hard wall. The bulk phase behavior and the substrate-adsorbate interaction are modeled by the free-volume theory for ideal polymers. The large size of the colloidal particles and the suppression of the van der Waals interaction by optical matching of colloid and solvent justify the planar hard wall model for the substrate. Following the Fisher-Jin scheme, we derive from the free-energy functional an interface potential V(l) for these mixtures. For a particle diameter of 10-100 nm, the calculations indicate a line tension tau approximately 10(-12)-10(-13) N at room temperature. In view of the ultralow interfacial tension in colloid-polymer mixtures, gamma approximately 10(-7) Nm, this leads to a rather large characteristic length scale taugamma in the micrometer range for the three-phase contact zone width. In contrast with molecular fluids, this zone could be studied directly with optical techniques such as confocal scanning laser microscopy.