Biology subjects

Parmeggiani, A.

Publications and source records attributed to Parmeggiani, A..

7 recordsLinked to original sources

bioRxiv2024

Quantitative model and physical mechanisms of iRBC membrane curling during egress of malaria parasites

Egress of malaria merozoites from infected red blood cells (iRBC) is a critical step in the parasites life cycle. The egress is accompanied by the formation of a pore in the erythrocyte membrane, followed by an outward curling of the membrane around the pore, resulting in a complete eversion of the erythrocyte membrane, pushing the parasites away. Despite the well-documented steps of the egress, the detailed mechanism and source of energy for such a spectacular eversion of iRBC remains largely unknown. In this paper, we consider a biophysical model based on the energetics of the egress process that includes both viscous dissipation and energy consumption for the formation of the rim around the pore in iRBC. We show that viscosity does not play a significant role in iRBC eversion and we hypothesize that this process is controlled by lateral lipid diffusion. The model is supported by quantitative estimates and is in good agreement with known experimental data.

biophysics↗

bioRxiv2023

Chromatin structure from high resolution microscopy: scaling laws and microphase separation

Recent advances in experimental fluorescence microscopy allow high accuracy determination (resolution of 50 nm) of the 3D physical location of multiple (up to [~] 102) tagged regions of the chromosome. We investigate publicly available microscopy data for two loci of the human Chr.21 obtained from multiplexed FISH methods for different cell lines and treatments. Inspired by polymer physics models, our analysis centers around distance distributions between different tags, aiming to unravel the chromatin conformational arrangements. We show that for any specific genomic site, there are (at least) two different conformational arrangements of chromatin, implying coexisting distinct topologies which we refer to as phase and phase {beta}. These two phases show different scaling behaviors: the former is consistent with a crumpled globule while the latter indicates a confined, but more extended conformation, as a looped domain. The identification of these distinct phases sheds light on the coexistence of multiple chromatin topologies and provides insights into the effects of cellular context and/or treatments on chromatin structure.

biophysics↗

bioRxiv2021

Relaxation time asymmetry in stator dynamics of the bacterial flagellar motor

The bacterial flagellar motor (BFM) is the membrane-embedded rotary molecular motor which turns the flagellum that provides thrust to many bacterial species. This large multimeric complex, composed of a few dozen constituent proteins, has emerged as a hallmark of dynamic subunit exchange. The stator units are inner-membrane ion channels which dynamically bind and unbind to the peptidoglycan at the rotor periphery, consuming the ion motive force (IMF) and applying torque to the rotor when bound. The dynamic exchange is known to be a function of the viscous load on the flagellum, allowing the bacterium to dynamically adapt to its local viscous environment, but the molecular mechanisms of exchange and mechanosensitivity remain to be revealed. Here, by actively perturbing the steady-state stator stoichiometry of individual motors, we reveal a stoichiometry-dependent asymmetry in stator remodeling kinetics. We interrogate the potential effect of next-neighbor interactions and local stator unit depletion and find that neither can explain the observed asymmetry. We then simulate and fit two mechanistically diverse models which recapitulate the asymmetry, finding stator assembly dynamics to be particularly well described by a two-state catch-bond mechanism.

biophysics↗

bioRxiv2020

Physical modeling of a sliding clamp mechanism for the spreading of ParB at short genomic distance from bacterial centromere sites

Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation have recently been shown to belong to a new class of CTP-dependent molecular switches. Strikingly, CTP binding and hydrolysis was shown to induce a conformational change enabling ParB dimers to switch between an open and a closed conformation. This latter conformation clamps ParB dimers on DNA molecules, allowing their diffusion in one dimension along the DNA. It has been proposed that this novel sliding property may explain the spreading capability of ParB over more than 10-Kb from parS centromere sites where ParB is specifically loaded. Here, we modeled such a mechanism as a typical reaction-diffusion system and compared this Clamping & sliding model to the ParB DNA binding pattern from high-resolution ChIP-sequencing data. We found that this mechanism cannot account for all the in vivo characteristics, especially the long range of ParB binding to DNA. In particular, it predicts a strong effect from the presence of a roadblock on the ParB binding pattern that is not observed in ChIP-seq. Moreover, the rapid assembly kinetics observed in vivo after the duplication of parS sites is not easily explained by this mechanism. We propose that Clamping & sliding might explain the ParB spreading pattern at short distances from parS but that another mechanism must apply for ParB recruitment at larger genomic distances.

systems biology↗

bioRxiv2019

ATP-driven separation of liquid phase condensates in bacteria

Liquid-liquid phase separated (LLPS) states are key to compartmentalise components in the absence of membranes, however it is unclear whether LLPS condensates are actively and specifically organized in the sub-cellular space and by which mechanisms. Here, we address this question by focusing on the ParABS DNA segregation system, composed of a centromeric-like sequence (parS), a DNA-binding protein (ParB) and a motor (ParA). We show that parS-ParB associate to form nanometer-sized, round condensates. ParB molecules diffuse rapidly within the nucleoid volume, but display confined motions when trapped inside ParB condensates. Single ParB molecules are able to rapidly diffuse between different condensates, and nucleation is strongly favoured by parS. Notably, the ParA motor is required to prevent the fusion of ParB condensates. These results describe a novel active mechanism that splits, segregates and localises non-canonical LLPS condensates in the sub-cellular space.

cell biology↗

bioRxiv2019

Mechanical instabilities of aorta drive blood stem cell production: a live study

During embryogenesis of all vertebrates, haematopoietic stem/progenitor cells (HSPCs) extrude from the aorta by a complex process named Endothelial-to-Haematopoietic Transition (EHT). HSPCs will then colonize haematopoietic organs allowing haematopoiesis throughout adult life. The mechanism underlying EHT including the role of each aortic endothelial cell within the global aorta dynamics remains unknown. In the present study, we show for the first time that EHT involves the remodelling of individual cells within a collective migration of endothelial cells which is tightly orchestrated, resulting in HSPCs extrusion in the sub-aortic space without compromising aorta integrity. By performing a cross-disciplinary study which combines high resolution 4D imaging and theoretical analysis based on the concepts of classical mechanics, we propose that this complex developmental process is dependent on mechanical instabilities of the aorta preparing and facilitating the extrusion of HSPCs.

developmental biology↗

bioRxiv2018

Robust and conserved stochastic self-assembly mechanism for dynamic ParB-parS partition complexes on bacterial chromosomes and plasmids

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 plasmid F 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) does not directly involve ParA, (ii) results in a dynamic structure of discrete size independent of ParB concentration, and (iii) 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.

systems biology↗