Biology subjects

Cluzel, P.

Publications and source records attributed to Cluzel, P..

8 recordsLinked to original sources

bioRxiv2026

Inherited flagellar structures coordinate the onset of swimming among related E. coli cells

Bacteria commit to costly behaviors before they can benefit from them. In Escherichia coli, flagellar synthesis is expensive, yet the genes are expressed in stochastic pulses and only a small minority of pulses result in motility. Despite this noise, we find that lineage-related cells begin swimming at similar times, in groups of two to eight cells. Rare, high-amplitude pulses commit a single cell within one generation, but more commonly, pulses rise slowly and fail to trigger swimming before division. Rather than decaying, their output accumulates as cells inherit hook-basal bodies (HBBs) and continue to build new ones. This structural inheritance acts as a physical integrator, summing ongoing transcriptional activity across generations, so that an incomplete flagellar cascade is carried forward at division rather than lost. HBB accumulation sets when cells swim, and the anti-sigma factor FlgM sets how sharply. By holding late flagellar genes off until several HBBs have accumulated, FlgM makes motility depend steeply on early flagellar gene expression, so that relatives inheriting similar sets of HBBs become motile together. Without FlgM, this sharp dependence is largely lost, and activations of the full cascade do not reliably produce swimming. Together, our results show how the accumulation of a molecular machine integrates fluctuations, and how a checkpoint on its assembly sharpens them into a decision, setting both the speed and heritability of a behavioral trait.

systems biology↗

bioRxiv2024

Stochastic Growth Bursts Enable Burden-Free Flagellum Production in a Single Bacterium

The cost of expressing unnecessary genes on growth has been explained at the population level through balanced growth assumptions. However, due to the high degree of stochasticity in growth and gene regulation, it remains unclear how classical growth laws derived from bulk measurements manifest at the level of individual cells. For example, flagellar gene expression, one of the most energy-intensive processes in E. coli, is typically associated with reduced growth rates in bulk measurements. By contrast, we find at the single-cell level that a strikingly opposite behavior coexists: flagellar gene activity is associated with an increase in growth rate. We show that this apparent contradiction, reminiscent of Simpsons paradox, results from examining in each cell instantaneous growth and gene expression without indiscriminately aggregating the single-cell data like in bulk measurements. We attribute this unrecognized behavior to out-of-balance growth boosts that temporarily offset the burden of flagellum production, likely driven by a surplus of growth factors inherited across cell division. Furthermore, we show that this non-intuitive relationship between growth and gene expression at the single-cell level is general, as we observe similar effects with synthetic systems driving the expression of fluorescent proteins downstream of constitutive promoters. Finally, we use a computational model to show that the inheritance of parental growth factors can explain the apparent contradiction and constitutes a general mechanism for mitigating the short-term cost of nonessential and biosynthetically demanding genes in the single cell.

molecular biology↗

bioRxiv2022

Monitoring lineages of growing and dividing bacteria reveals an inducible memory of mar operon expression

In Gram negative bacteria, the multiple antibiotic resistance or mar operon, is known to control the expression of multi-drug efflux genes that protect bacteria from a wide range of drugs. Since different drugs induce this response, identifying the parameters that govern the dynamics of its induction is crucial to better characterize the process of tolerance and resistance. Most experiments have assumed that the properties of the mar transcriptional network can be inferred from population measurements. However, measurements from an asynchronous population of cells can mask underlying phenotypic variations of single cells. We monitored the activity of the mar promoter in single Escherichia coli cells in linear micro-colonies and established that the response to a steady level of inducer was heterogeneous within individual colonies. Specifically, sub-lineages defined by contiguous daughter-cells exhibited similar promoter activity, whereas activity was greatly variable between different sub-lineages. Specific sub-trees of uniform promoter activity persisted over several generations. Statistical analyses of the lineages suggest that the presence of these sub-trees is the signature of an inducible memory of the promoter state that is transmitted from mother to daughter cells. This single-cell study reveals that the degree of epigenetic inheritance changes as a function of inducer concentration, suggesting that phenotypic inheritance may be an inducible phenotype.

systems biology↗

bioRxiv2021

Robustness of DNA Looping Across Multiple Divisions in Individual Bacteria

DNA looping has emerged as a central paradigm of transcriptional regulation as it is shared across many living systems. One core property of DNA looping-based regulation is its ability to greatly enhance repression or activation of genes with only a few copies of transcriptional regulators. However, this property based on small number of proteins raises the question of the robustness of such a mechanism with respect to the large intracellular perturbations taking place during growth and division of the cell. Here we address the issue of sensitivity to variations of intracellular parameters of gene regulation by DNA looping. We use the lac system as a prototype to experimentally identify the key features of the robustness of DNA looping in growing E. coli cells. Surprisingly, we observe time intervals of tight repression spanning across division events, which can sometimes exceed ten generations. Remarkably, the distribution of such long time intervals exhibits memoryless statistics that is mostly insensitive to repressor concentration, cell division events, and the number of distinct loops accessible to the system. By contrast, gene regulation becomes highly sensitive to these perturbations when DNA looping is absent. Using stochastic simulations, we propose that the robustness to division events of memoryless distributions emerges from the competition between fast, multiple re-binding events of repressors and slow initiation rate of the RNA-polymerase. We argue that fast re-binding events are a direct consequence of DNA looping that ensures robust gene repression across a range of intracellular perturbations. Significance statementIt is well-established that certain intracellular regulators can stabilize DNA loops to greatly enhance activation or repression of gene transcription. In vitro but also in vivo ensemble measurements have determined that only a few copies of regulators are in fact needed to stably form DNA loops. In view of such a small number, we address the issue of sensitivity of gene regulation by DNA looping to variations of intracellular parameters in individual growing E. coli bacteria. Surprisingly, we find that DNA looping from the lac system is robust to a range of perturbations including divisions during which cells can maintain tight repression over many generations. We propose a mechanism that governs the observed robustness across a range of intracellular perturbations.

biophysics↗

bioRxiv2021

Resonant Learning in Scale-free Networks

Over the last decades, analyses of the connectivity of large biological and artificial networks have identified a common scale-free topology, where few of the network elements, called hubs, control many other network elements. In monitoring the dynamics of networks hubs, recent experiments have revealed that they can show behaviors oscillating between on and off states of activation. Prompted by these observations, we ask whether the existence of oscillatory hubs states could contribute to the emergence of specific network dynamical behaviors. Here, we use Boolean threshold networks with scale-free architecture as representative models to demonstrate how periodic activation of the network hub can provide a network-level advantage in learning specific new dynamical behaviors. First, we find that hub oscillations with distinct periods can induce robust and distinct attractors whose lengths depend upon the hub oscillation period. Second, we determine that a given network can exhibit series of different attractors when we sequentially change the period of hub pulses. Using rounds of evolution and selection, these different attractors could independently learn distinct target functions. We term this network-based learning strategy resonant learning, as the emergence of new learned dynamical behaviors depends on the choice of the period of the hub oscillations. Finally, we find that resonant learning leads to convergence towards target behaviors over an order of magnitude faster than standard learning procedures. While it is already known that modular network architecture contributes to learning separate tasks, our results reveal an alternative design principle based on forced oscillations of the network hub. SIGNIFICANCELarge networks of interconnected components such as genes or machines can coordinate complex behavioral dyamics. One outstanding question has been to identify the design principles that allow networks to learn new behaviors. Here, in simulating learning cycles, we randomly modify the interactions between components and select networks that exhibit a desired behavior. Surprisingly, we find that networks can learn new behaviors faster when the state of the most connected network component is forced to oscillate during learning. Remarkably, using distinct periods of oscillations allows a given network to learn distinct behaviors. While it is known that modular network architecture contributes to learning separate tasks, our results reveal an alternative design principle for which modules are not needed.

biophysics↗

bioRxiv2020

A filter-and-integrate mechanism generates stochastictranscriptional pulses in E.coli flagellar synthesis

Stochastic pulsatile dynamics have been observed in an increasing number of biological circuits with typical mechanism involving feedback control. Surprisingly, recent single-cell experiments showed that E. coli flagellar class-2&3 promoters are activated in stochastic pulses without the means of feedback, however, the underlying design principles of pulse generation have remained unclear. Here, by developing a system-level stochastic model constrained by a large set of E. coli flagellar synthesis data from different strains and mutants, we identify the underlying design principles for generating stochastic transcriptional pulses without feedback. Our model shows that YdiV, an inhibitor of the class-1 master regulator (FlhDC), creates an ultrasensitve switch that serves as a digital filter to eliminate small amplitude FlhDC fluctuations. Additionally, we demonstrate that fast temporal fluctuations of FlhDC are smoothed out and integrated over time before affecting class-2 downstream genes. Together, our results reveal the existence of a filter-and-integrate design that is necessary for generating stochastic pulses without feedback. This strategy suggests that E. coli may avoid premature activation of the expensive flagellar gene expression by filtering input fluctuations in intensity and in time.

microbiology↗

bioRxiv2018

Pulsating transcriptional dynamics generates cell-to-cell variability in E. coli flagellum synthesis

The classic picture of flagellum biosynthesis in E. coli, inferred from population measurements, describes a tightly controlled, deterministic transcriptional program. In individual E. coli cells, we discover that flagellar promoters are in fact stochastically activated in pulses. Such pulses comprise coordinated on and off states of promoter activity, each of which can span multiple generations. We demonstrate that this pulsing program obeys the regulatory logic of flagellar assembly, which dictates whether some promoters skip pulses. Remarkably, pulses in this transcriptional network appear to be actually governed by a post-translational circuit. Our results suggest that even topologically simple transcriptional networks can generate unexpectedly rich temporal dynamics and phenotypic heterogeneities.

microbiology↗

bioRxiv2018

Codon-dependent noise dictates cell-to-cell variability in nutrient poor environments

Under nutrient-rich conditions, stochasticity of transcription drives protein expression noise. However, by shifting the environment to amino acid-limited conditions, we identified in E. coli a source of noise whose strength is dictated by translational processes. Specifically, we discovered that cell-to-cell variations in fluorescent protein expression depend on codon choice, with codons yielding lower mean expression after amino acid downshift also resulting in greater noise. We propose that ultra-sensitivity in the tRNA charging/discharging cycle shapes the strength of the observed noise by amplifying fluctuations in global intracellular parameters, such as the concentrations of amino acid, synthetase, and tRNA. We hypothesize that this codon-dependent noise may allow bacteria to selectively optimize cell-to-cell variability in poor environments without relying on low molecular numbers.

systems biology↗