Biology subjects

Vaknin, A.

Publications and source records attributed to Vaknin, A..

5 recordsLinked to original sources

bioRxiv2025

Single-array measurements reveal non-uniform, mosaic-like chemosensory arrays in bacteria

Motile bacteria use supramolecular arrays to detect effector gradients in their environment. In Escherichia coli, thousands of chemoreceptor molecules with diverse sensory properties cooperatively modulate the kinase activity of these arrays and, via phosphotransfer to a diffusible response regulator, control the cells swimming behavior. Various methods have been used to study these sensory arrays in live cells, from population-level assays to single-cell measurements, revealing hierarchical coupling interactions that underlie their remarkable sensory properties. However, measuring the responses of individual arrays has remained a challenge. Here, by combining the kinase and response regulator into a functional hybrid protein that resides within the array, we directly measured the kinase responses of individual arrays in live cells. These measurements revealed highly diverse and growth-phase-dependent sensory properties of individual arrays. Even arrays within the same cell were not substantially correlated. We also observed dynamic shifts in receptor occupancy within individual arrays. Overall, these data suggest that each array contains a frozen non-uniformity, reflecting its unique assembly history and resulting in a mosaic arrangement of cooperative signaling regions, each with distinct receptor content. Consistent with this view, measured dose-responses of individual arrays mostly exhibit low cooperativity. Interestingly, signal integration in such non-uniform arrays is expected to inherently vary with the size of the cooperative regions.

biophysics↗

bioRxiv2025

Emergence of active turbulence limits chemotaxis-induced collective condensation of bacteria

Collective bacterial condensation arises from positive feedback between the ability of bacteria to generate chemical gradients in their environment and their chemotactic ability to follow those gradients. This feedback drives the spontaneous formation of local cell accumulations, characterized by sharp cell-density gradients, even in the absence of physical boundaries. By following the dynamics of bacterial condensation in uniform acidic environments, we show that condensation is critically constrained by the spontaneous emergence of correlated bacterial swimming and the associated active turbulence. These collective behaviors generate vortex-like cell motion with a pronounced radial component directed down the cell-density gradient. This, in turn, induces local fluid motion that broadens the condensate and expels non-chemotactic bacteria. When condensates are strongly confined in thin layers, the radial component of fluid motion diminishes and condensation is enhanced. Moreover, in porous environments, correlated bacterial motion is strongly suppressed, allowing spontaneous condensation to progress even further until it reaches the limits imposed by the non-local nature of bacterial chemotaxis. Overall, these findings highlight the fundamental interplay between self-generated bacterial condensation and correlated swimming. Significance statementSelf-induced condensation and active turbulence are two prominent forms of collective bacterial behaviors. However, their interplay has not been experimentally studied. Here, we show that collective bacterial condensation gives rise to correlated swimming, which in turn fundamentally limits further condensation. Furthermore, we demonstrate that in dilute porous environments--common in natural bacterial habitats--correlated swimming is strongly suppressed, enabling the spontaneous formation of extremely dense cell condensates. These condensates may serve as a basis for the development of more structured bacterial communities.

biophysics↗

bioRxiv2025

A Plasma Membrane Vesicle Imaging-Based Platform for Studying Membrane Fusion

Membrane fusion is central to biological processes such as viral entry, fertilization and cell-to-cell fusion. Gaining a mechanistic understanding of fusion requires the ability to visualize and quantify the dynamic interaction between two membranes and their associated protein machineries at high temporal and spatial resolution. However, studying these processes in live cells remains challenging due to the complexity of the cellular environment. Here we demonstrate a versatile cell-free platform based on giant plasma membrane vesicles (GPMVs) that enables controlled, quantitative analysis of receptor binding and membrane fusion kinetics in a native membrane context. As proof of concept, we reconstitute the SARS-CoV-1 Spike-ACE2 interaction, capturing specific receptor engagement and accumulation at the membrane interface using confocal microscopy and micropipette aspiration. Fusion was induced by proteolytic activation and quantified using both high-resolution microscopy and high-throughput Imaging Flow Cytometry. The platform also reveals the influence of membrane composition on fusion efficiency, demonstrated by the impact of cholesterol depletion. This approach provides a broadly applicable system for dissecting membrane fusion and protein-protein interactions across membranes, with compatibility for biophysical, imaging and structural analysis. It offers new opportunities for mechanistic studies and inhibitor screening in a biologically relevant yet experimentally accessible context.

biophysics↗

bioRxiv2023

Chloride intracellular channel (CLIC) proteins function as fusogens

Chloride Intracellular Channel (CLIC) family members uniquely transition between soluble and membrane-associated conformations. Despite decades of extensive functional and structural studies, CLICs function as ion channels remains debated, rendering our understanding of their physiological role incomplete. Here, we expose a novel function of CLIC5 as a fusogen. We demonstrate that purified CLIC5 directly interacts with the membrane and induces fusion, as reflected by increased liposomal diameter and lipid and content mixing between liposomes. Moreover, we show that this activity is facilitated by acidic pH, a known trigger for CLICs transition to a membrane-associated conformation, and that increased exposure of the hydrophobic inter-domain interface is crucial for this process. Finally, mutation of a conserved hydrophobic interfacial residue diminishes the fusogenic activity of CLIC5 in vitro and impairs excretory canal extension in C. elegans in vivo. Together, our results unravel the long-sought physiological role of these enigmatic proteins.

biochemistry↗

bioRxiv2017

Multiple Sources Of Signaling Noise In Bacterial Chemotaxis Network

Cellular networks are intrinsically subject to stochastic fluctuations, but analysis of the resulting noise remained largely limited to gene expression. The pathway controlling chemotaxis of Escherichia coli provides one example where posttranslational signaling noise has been deduced from cellular behavior. This noise was proposed to result from stochasticity in chemoreceptor methylation, and it is believed to enhance environment exploration by bacteria. Here we combined single-cell FRET measurements with analysis based on the fluctuation-dissipation theorem (FDT) to characterize origins of activity fluctuations within the chemotaxis pathway. We observed surprisingly large methylation-independent thermal fluctuations of receptor activity, which contribute to noise comparably to the energy-consuming methylation dynamics. Interactions between clustered receptors involved in amplification of chemotactic signals are also necessary to produce the observed large activity fluctuations. Our work thus shows that the high response sensitivity of this cellular pathway also increases its susceptibility to noise, from thermal and out-of-equilibrium processes.

systems biology↗