Biology subjects

Colin, R.

Publications and source records attributed to Colin, R..

12 recordsLinked to original sources

bioRxiv2026

Antagonistic small proteins enable magnesium-dependent tuning of two-component signaling

Small proteins are emerging regulators of bacterial virulence via signaling pathways. However, how multiple small proteins coordinate to control a single pathway remains unclear. Here we show that two antagonistic small proteins, SafA and MgrB, forming a magnesium-dependent control module, enhance the signaling sensitivity of the PhoQ/PhoP two-component system in E. coli. Leveraging conditions that enable sequential expression of SafA and MgrB, we dissect and characterize their regulatory dynamics. Our results reveal magnesium as the central control parameter modulating the abundance and affinities of the small proteins for the sensor kinase PhoQ. This coupling together with the competitive binding of the small proteins enables self-adjustment of the signaling network and enhances its sensitivity to environmental magnesium changes. Functionally, loss of either small proteins influences the ability of enteropathogenic E. coli to evade macrophage phagocytosis, linking this regulatory scheme to host interaction. Our findings establish a framework for achieving a high level of input sensitivity through antagonistic regulations in a signaling network.

microbiology↗

bioRxiv2025

Active bacterial pattern formation in evaporating droplets

Bacteria living on surfaces are often confined to droplets. When these droplets evaporate, the motion of the liquid-air interface and the associated internal capillary flow confine the bacteria. Here we study how E. coli bacteria interact with this capillary confinement and agglomerate at the droplets contact line. We identify three different types of bacterial pattern formation that depend on the bacterial activity and the environmental conditions imposed by the evaporating droplet. When the evaporation is fast, the bacteria are slow or the suspension is dilute, a uniform contact-line deposit forms. However, when the capillary confinement concentrates the bacteria at the contact line beyond a critical number density, localized collective motion spontaneously emerges. In that case, the bacteria induce a local stirring of the liquid that allows them to self-organize into periodic patterns and enables them to collectively escape from the contact line. At very high number densities, these periodic patterns get destabilized by bacterial turbulence in the bulk of the droplet resulting in the formation of mobile bacterial plumes at the contact line. Our results show how the subtle interplay between the bacteria and the capillary flow inside the droplet that surrounds them governs their dispersal. Significance StatementAn evaporating sessile droplet is a common natural habitat to bacteria. Bacteria that live inside the droplet are exposed to a confinement caused by the moving liquidair interface, and an evaporation-driven capillary flow that agglomerates them at the contact line. Here we show how bacteria interact with this confining flow. We identify three vastly different types of bacterial self-organization that depend on the bacterial activity and the environmental conditions imposed by the droplet. Our work is a first step towards understanding how the interplay between motile bacteria and the interfacial flows that exist in evaporating droplets affects their deposition onto surfaces, which is key to their future survival.

biophysics↗

bioRxiv2024

Role of a single MCP in evolutionary adaptation of Shewanella putrefaciens for swimming in planktonic and structured environments

Bacteria can adapt to their environments by changing phenotypic traits by mutations. However, improving one trait often results in deterioration of another one, a trade-off which limits the degree of adaption. The gammaproteobacterium Shewanella putrefaciens CN-32 has an elaborate motility machinery comprising two distinct flagellar systems and an extensive chemotaxis array with 36 methyl-accepting chemotaxis sensor proteins (MCPs). In this study we performed experimental selection on S. putrefaciens for increased spreading through a porous environment. We readily obtained a mutant that showed a pronounced increase in covered distance. This phenotype was almost completely caused by a deletion of 24 bp from the chromosome, which leads to a moderately enhanced production of a single MCP. Accordingly, chemotaxis assays under planktonic conditions and cell tracking in soft agar showed that the mutation improved navigation through nutritional gradients. The study demonstrates how differences in the abundance of a single MCP can lead to an efficient upgrade of directed flagella-mediated motility in specific environments at a low expense of cellular resources. ImportanceExperimental evolution experiments have been used to determine the trade-offs occurring in specific environments. Several studies that have used the spreading behavior of bacteria in structured environments identified regulatory mutants that increase the swimming speed of the cells. While this results in a higher chemotaxis drift, the growth fitness decreases as the higher swimming speed requires substantial cellular resources. Here we show that rapid chemotaxis adaptation can also be achieved through modification of the chemotaxis signal input at a low metabolic cost for the cell.

microbiology↗

bioRxiv2024

Swarming bacteria exhibit developmental phase transitions to establish scattered colonies in new regions

The bacterial Type 9 Secretion System (T9SS) is essential for the development of periodontal diseases and Bacteroidetes gliding motility. T9SS-driven motile bacteria, abundant within the human oral microbiota, transport non-motile oral microbes and bacteriophages as cargo, shaping the spatial structure of polymicrobial communities. However, the physical rules governing the dispersal of T9SS-driven bacterial swarms are barely understood. Here, we collected time-lapse images, under anaerobic conditions, of developing swarms of a T9SS-driven microbe common to the human oral microbiota. Tracking of swarms revealed that small peripheral flares emerging from a colony develop structures that resemble fireworks displaying a chrysanthemum effect and flower-like patterns that convert to wave-like patterns and which further evolve into scattered microcolonies. Particle-image velocimetry showed density-dependent phase transitions and initial vorticity within these emerging patterns. Numerical simulations demonstrate that these patterns arise due to changes in swarm speed and alignment strength. Our data reveal a strategy used by an anaerobic swarming bacterium to control swarm behavior, resulting in scattered microcolonies distant from the mother colony, thus reducing competition for resources among colony members. This might ensure species survival even if conditions change drastically in one location of the human oral cavity.

microbiology↗

bioRxiv2024

Active segregation in binary mixtures under flow

Many bacterial habitats, from the gut to the soil, feature narrow channels where confined flow is a key constraint that might influence the spatial organization, and thus the functioning, of the complex, phenotypically heterogeneous communities these microbes form. Here, we investigate how a model heterogeneous bacterial community of motile and non-motile Escherichia coli organizes under confined Poiseuille flow. We discovered a new mode of active self-organization, where the motile bacteria induce the rapid sideways segregation of the non-motile cells to one side of the channel, eventually resulting in asymmetric biofilm formation. Our experiments and modeling elucidated the purely physical segregation mechanism: the rheotactic drift of the motile cells, which stems from shear acting on their chiral flagella, induces a conveyer-belt-like backflow advecting the non-motile cells. The latter then accumulate thanks to sedimentation countering flow incompressibility. This unexpected consequence of motility can affect the organization of complex bacteria communities colonizing environments under confined flow.

biophysics↗

bioRxiv2024

Physics and physiology determine strategies of bacterial investment in flagellar motility

Regulatory strategies that allow microorganisms to balance their investment of limited resources in different physiological functions remain poorly understood, particularly for numerous cellular functions that are not directly required for growth. Here, we investigate the allocation of resources to flagellar swimming, the most prominent and costly behavior in bacteria that is not directly required for growth. We show that the dependence of motile behavior on gene expression in Escherichia coli is determined by the hydrodynamics of propulsion, which limits the ability of bacteria to increase their swimming by synthesizing more than a critical number of flagellar filaments. Together with the fitness cost of flagellar biosynthesis, this defines the physiologically relevant range of investment in motility. Gene expression in all E. coli isolates tested falls within this range, with many strains maximizing motility under nutrient-rich conditions, particularly when grown on a porous medium. The hydrodynamics of swimming may further explain the bet-hedging behavior observed at low levels of motility gene expression.

microbiology↗

bioRxiv2024

Experimental evolution of a reduced bacterial chemotaxis network

Chemotaxis allows bacteria to follow chemical gradients by comparing their environment over time and adjusting their swimming behavior accordingly. The chemotaxis signaling pathway is highly conserved among all chemotactic bacteria. The system comprises two modules: one for environmental sensing and signal transduction toward the flagellar motor, and the other for adapting to the constant level of background stimulation and providing short-term memory for temporal comparisons. Previous experimental analysis and mathematical modeling have suggested that all components of the paradigmatic chemotaxis pathways in Escherichia coli are essential. This indicates that it may contain a minimal set of protein components necessary to mediate gradient sensing and behavioral response. To test this assumption, here we subjected strains carrying deletions in chemotaxis genes to experimental laboratory evolution. We observed that the core components of the chemotaxis pathway are indeed essential. However, the absence of individual auxiliary pathway proteins, including the adaptation enzymes that are conserved in a vast majority of bacteria, and the phosphatase, could be compensated for to varying degrees by changes in other pathway components. Our results suggest that the experimental evolution of these deletion strains has led to the emergence of alternative strategies for bacterial chemotaxis, demonstrating the surprisingly rapid evolvability of this signaling network.

microbiology↗

bioRxiv2023

Active density fluctuations in bacterial binary mixtures

In wild environments, physical and biochemical interactions between intermixed motile and sessile microorganisms give rise to spatial organization that is key for the functioning and ecology of complex communities. However, how motility-driven physical interactions contribute to shaping multispecies communities remains little understood. To address this gap, we investigated model binary mixtures of motile and non-motile Escherichia coli bacteria. We discovered a new type of non-equilibrium self-organization, wherein large-scale density fluctuations of non-motile bacteria emerge when mixed with motile ones under physiologically relevant conditions. Systematically exploring the phase diagram in microfluidics experiments and combining them with modeling and simulations, we uncovered the two-pronged physical mechanism of emergence: Circular swimming of motile cells close to surfaces generates recirculating hydrodynamic flows that advect non-motile cells, while sedimentation, by breaking the vertical symmetry, is essential for their local accumulation. This active self-organization behavior in mixed bacterial populations appears crucial for complex microbial community structuration.

biophysics↗

bioRxiv2022

Exercise Training Remodels Adipocyte-Specific Extracellular Matrix Proteins and Alters Innervation and Vascularization in Inguinal White Adipose Tissue (iWAT)

Inguinal white adipose tissue (iWAT) is essential for the beneficial effects of exercise training on metabolic health. Extracellular matrix (ECM) composition, innervation, and vascularization are all important regulators of iWAT function, yet whether exercise training improves these structural components of iWAT is unknown. Using biochemical, imaging, and multi-omics analyses we find that 11-days of wheel running in male mice causes profound iWAT remodeling including decreased ECM deposition and increased vascularization and innervation. We identify adipose stem cells as the main contributors to training-induced ECM remodeling, determine that training causes a shift from hypertrophic to insulin-sensitive adipocyte subpopulations, show that the PRDM16 transcriptional complex is necessary for iWAT remodeling and beiging, and discover neuronal growth regulator 1 (NEGR1) as a link between PRDM16 and neuritogenesis. Exercise training leads to remarkable adaptations to iWAT structure and cell-type composition that can confer beneficial changes in tissue metabolism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/503375v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@fd590eorg.highwire.dtl.DTLVardef@e1dd02org.highwire.dtl.DTLVardef@74be24org.highwire.dtl.DTLVardef@6f6e58_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2022

Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions and cell growth

Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli, and, for the faster-diffusing proteins, it is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.

biophysics↗

bioRxiv2018

Chemotactic behavior of Escherichia coli at high cell density

At high cell density, swimming bacteria exhibit collective motility patterns, self-organized through physical interactions of a however still debated nature. Although high-density behaviours are frequent in natural situations, it remained unknown how collective motion affects chemotaxis, the main physiological function of motility, which enables bacteria to follow environmental gradients in their habitats. Here, we systematically investigate this question in the model organism Escherichia coli, varying cell density, cell length, and suspension confinement. The characteristics of the collective motion indicate that hydrodynamic interactions between swimmers made the primary contribution to its emergence. We observe that the chemotactic drift is moderately enhanced at intermediate cell densities, peaks, and is then strongly suppressed at higher densities. Numerical simulations reveal that this suppression occurs because the collective motion disturbs the choreography necessary for chemotactic sensing. We suggest that this physical hindrance imposes a fundamental constraint on high-density behaviours of motile bacteria, including swarming and the formation of multicellular aggregates and biofilms.

biophysics↗

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↗