Biology subjects

Geniet, F.

Publications and source records attributed to Geniet, F..

4 recordsLinked to original sources

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

Modelling the Perception of Colour Patterns in Vertebrates with HMAX

O_LIIn order to study colour signals as animals perceive them, visual ecologists usually rely on models of colour vision that do not consider patterns-the spatial arrangement of features within a signal. C_LIO_LIHMAX describes a family of models that are used to study pattern perception in human vision research, and which have inspired many artificial intelligence algorithms. In this article, we highlight that the sensory and brain mechanisms modelled in HMAX are widespread, occurring in most if not all vertebrates, thus offering HMAX models a wide range of applications in visual ecology. C_LIO_LIWe begin with a short description of the neural mechanisms of pattern perception in vertebrates, emphasizing similarities in processes across species. Then, we provide a detailed description of HMAX, highlighting how the model is linked to biological vision. We further present sparse-HMAX, an extension of HMAX that includes a sparse coding scheme, in order to make the model even more biologically realistic and to provide a tool for estimating efficiency in information processing. In an illustrative analysis, we then show that HMAX performs better than two other reference methods (manually-positioned landmarks and the SURF algorithm) for estimating similarities between faces in a nonhuman primate species. C_LIO_LIThis manuscript is accompanied with MATLAB codes of an efficient implementation of HMAX and sparse-HMAX that can be further flexibly parameterized to model non-human colour vision, with the goal to encourage visual ecologists to adopt tools from computer vision and computational neuroscience. C_LI

evolutionary 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↗