9 research outputs found
Modelling the effect of ribosome mobility on the rate of protein synthesis
Translation is one of the main steps in the synthesis of proteins. It
consists of ribosomes that translate sequences of nucleotides encoded on mRNA
into polypeptide sequences of amino acids. Ribosomes bound to mRNA move
unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been
hypothesized that finite diffusion of ribosomes plays an important role in
ribosome recycling and that mRNA circularization enhances the efficiency of
translation. In order to estimate the effect of cytoplasmic diffusion on the
rate of translation, we consider a Totally Asymmetric Simple Exclusion Process
(TASEP) coupled to a finite diffusive reservoir, which we call the Ribosome
Transport model with Diffusion (RTD). In this model, we derive an analytical
expression for the rate of protein synthesis as a function of the diffusion
constant of ribosomes, which is corroborated with results from continuous-time
Monte Carlo simulations. Using a wide range of biological relevant parameters,
we conclude that diffusion in biological cells is fast enough so that it does
not play a role in controlling the rate of translation initiation.Comment: article, 16 pages, 5 figure
Erratum to: Modelling the effect of ribosome mobility on the rate of protein synthesis
A Correction to this paper has been published: 10.1140/epje/s10189-021-00019-
Surfing on protein waves: proteophoresis as a mechanism for bacterial genome partitioning
6 pages, 3 figuresInternational audienceEfficient 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 âvolumetricâ 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
Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex
International audienceParAB S , the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS , and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS -anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParB S complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS . In the SBM, DNA loops stochastically bring loci inside a sharp cluster of ParB. However, previous SBM versions did not include the negative supercoiling of bacterial DNA, leading to use unphysically small DNA persistences to explain the ParB binding profiles. In addition, recent super-resolution microscopy experiments have revealed a ParB cluster that is significantly smaller than previous estimations and suggest that it results from a liquid-liquid like phase separation. Here, by simulating the folding of long (â„ 30 kb) supercoiled DNA molecules calibrated with realistic DNA parameters and by considering different possibilities for the physics of the ParB cluster assembly, we show that the SBM can quantitatively explain the ChIP-seq ParB binding profiles without any fitting parameter, aside from the supercoiling density of DNA, which, remarkably, is in accord with independent measurements. We also predict that ParB assembly results from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., ParB clusters behave like liquid-like protein condensates with unconventional âleakyâ boundaries
A conserved mechanism drives partition complex assembly on bacterial chromosomes and plasmids
Synopsis Chromosome and plasmid segregation in bacteria are mostly driven by ParABS systems. These DNA partitioning machineries rely on large nucleoprotein complexes assembled on centromere sites (parS). However, the mechanism of how a few parS-bound ParB proteins nucleate the formation of highly concentrated ParB clusters remains unclear despite several proposed physico-mathematical models. We discriminated between these different models by varying some key parameters in vivo using the F plasmid partition system. We found that "Nucleation & caging" is the only coherent model recapitulating in vivo data. We also showed that the stochastic self-assembly of partition complexes (i) is a robust mechanism, (ii) does not directly involve ParA ATPase, (iii) results in a dynamic structure of discrete size independent of ParB concentration, and (iv) is not perturbed by active transcription but is by protein complexes. We refined the "Nucleation & caging" model and successfully applied it to the chromosomally encoded Par system of Vibrio cholerae, indicating that this stochastic self-assembly mechanism is widely conserved from plasmids to chromosomes
Poétisation de l'histoire et de la politique
Ce numĂ©ro sur « PoĂ©tisation de lâhistoire et de la politique » sâinscrit dans le cadre de lâaxe culturel, portant sur les reprĂ©sentations sociales et textuelles de rĂ©alitĂ©s historiques et politiques, de lâĂ©quipe du MIMMOC (EA 3812). Ses Ă©diteurs se penchent sur lâinteraction entre des champs disciplinaires diffĂ©rents : lâhistoire (ses traces, sa perception, son Ă©criture, ses reprĂ©sentations) et son esthĂ©tisation, quâils ont qualifiĂ©e de poĂ©tisation, du point de vue rhĂ©torique, graphique ou iconographique, quâil sâagisse de peinture, de cinĂ©ma ou de toute autre reprĂ©sentation par lâimage. Sâappuyant dâune part sur le concept dĂ©sormais bien Ă©tabli du « lieu de mĂ©moire » dans ses deux acceptions, matĂ©rielle et immatĂ©rielle, dĂ©veloppĂ©es par Pierre Nora et ses successeurs, mais aussi sur le concept de « poĂ©sie » et dâ « aura » dĂ©fini par Walter Benjamin Ă propos de lâĆuvre dâart, puis revisitĂ© par les travaux de Paul Ricoeur et de Roland Barthes sur lâicĂŽne et lâimage (notamment la photographie), un groupe de chercheurs issus de plusieurs champs disciplinaires (Ă©tudes anglo-amĂ©ricaines, germaniques, hispaniques, italiennes, lusophones, nĂ©o-hellĂ©niques, slaves, mais aussi histoire contemporaine, lettres modernes ou littĂ©rature comparĂ©e), sâest rĂ©uni pour analyser le lien entre lâĂ©vĂ©nement et son esthĂ©tisation et les correspondances entre les divers domaines impliquĂ©s. Le numĂ©ro comporte quatre chapitres : le premier, « Histoire et Ă©criture » questionne lâĂ©criture de lâhistoire pour voir comment le rĂ©el est retranscrit ou interprĂ©tĂ© (3 articles, de JĂ©rĂŽme GrĂ©vy, Michel Riaudel et Sanja Boskovic). Le deuxiĂšme, « La poĂ©sie des lieux » (2 articles), porte sur la poĂ©sie qui Ă©mane des vestiges (GeneviĂšve Puig, Isabelle SolĂšres). Le troisiĂšme, « PoĂ©tisation artistique et littĂ©raire » (5 articles), sâintĂ©resse aux reprĂ©sentations littĂ©raires (Geoffrey Pitcher, Marie-Catherine Chanfreau, Elvire Diaz, Alix Mary-Tubman, Sandra Teixeira). Le dernier, « PoĂ©tisation en images et en twitt » (3 articles), porte sur le cinĂ©ma et sur twitter (Jeremy Price, Pascal Vacher, NoĂ©mie Suisse). This issue on "Poetising history and politics" follows the cultural studies research on social and textual representation of historical and political reality conducted within the MIMMOC research group (EA 3812). The editors have concentrated on the interaction between varied disciplinary fields : history (traces, perception, writing, representation) and its aesthetic value, which they have chosen to term 'poetising', in a rhetorical, graphic or iconographic from, whether painting, cinema or any other image form. Using on the one hand the well-established concept of "places of memory" in its two senses, both material and immaterial, developed by Pierre Nora and his followers, and on the other hand on the concept of "poetry" and "aura" defined by Walter Benjamin in respect of works of art, then reutilised in the works of Paul Ricoeur and Roland Barthes on the icone and images (in particular photography, a group of academics from several disciplinary fields (area studies - English, German, Spanish, Italian, Portuguese, Greek, Slavic - contemporary history, French literature, comparative literature), analyse both the link between an event and its aethestic translation and the interactions between the different fields involved. The issue is divided into four sections : the first, "History and writing" asks how the (re-)writing of history restranscribes or reinterprets reality (3 articles by JĂ©rĂŽme GrĂ©vy, Michel Riaudel et Sanja Boskovic). The second, "The poetry of place" (2 articles), looks at the poetry that emanates from ruins (GeneviĂšve Puig, Isabelle SolĂšres). The third part, "Artistic and literary poetising" (5 articles), looks at litterary representations (Geoffrey Pitcher, Marie-Catherine Chanfreau, Elvire Diaz, Alix Mary-Tubman, Sandra Teixeira). The final section, "Poetising in pictures and by tweet" (3 articles), concerns the film and twitter media (Jeremy Price, Pascal Vacher, NoĂ©mie Suisse)