Biology subjects

Proenca, A. M.

Publications and source records attributed to Proenca, A. M..

4 recordsLinked to original sources

bioRxiv2025

Population Consequences of Single-Cell Damage Dynamics: Theory and Experiment under Glucose Limitation in E. coli

Microbial population growth arises from the survival and division of individual cells. However, under environmental stress, how reduced population fitness emerges from the single-cell dynamics remains poorly understood. Cellular aging and damage accumulation are often overlooked in linking these levels. Here, we use both theory and experiment to investigate how stochastic and asymmetric damage dynamics shape population outcomes. Theoretically, we apply a jump-diffusion damage model within a structured population framework to explore the roles of damage rate, noise, and partitioning asymmetry. Our theoretical analyses show that these parameters influence population growth both at equilibrium and during transient dynamics, suggesting that their cellular regulation may be a key strategy for sustaining population fitness. Experimentally, we expose Escherichia coli to glucose limitation and monitor stress responses using a RpoS fluorescent reporter, tracking both single-cell behavior in a microfluidic device combined with time-lapse fluorescence microscopy and population growth in a plate reader. Glucose limitation leads to the effects of elevated stress, reduced division, and increased mortality, which are consistently observed across scales. Using parameter estimates from single-cell data, our model deepens insights on population-level dynamics and highlights damage-noise driven, damage-dependent mortality as a key factor under stress. Together, these findings establish a quantitative framework linking intracellular stress to population fitness under environmental stress.

evolutionary biology↗

bioRxiv2024

Protein aggregation drives cell aging in a size-specific manner in Escherichia coli

Aging, the decline in physiological function over time, is marked by the intracellular accumulation of damaged components. It can be attributed to a trade-off between the investment into organismal maintenance and the production of high-quality offspring, where the parent accumulates damage over time and retains it upon reproduction, while the offspring is rejuvenated. Asymmetric damage partitioning has been observed even in simple unicellular organisms, such as Escherichia coli bacteria, that retain aggregates of misfolded proteins during cell division. However, recent studies presented conflicting evidence on the effect of protein aggregates on fitness, ranging from detrimental effects on cell growth to enhanced stress survival. Here, we show that the decisive factor driving growth decline in E. coli is not the presence of a protein aggregate, but the proportion of the intracellular space occupied by it. By following single-cell E. coli lineages expressing fluorescently labeled DnaK chaperones, we quantified damage accumulation and partitioning across generations in microfluidic devices. Our results suggest that the aggregation of damaged proteins allows cells to keep damage separate from vital processes and compensate for the lost intracellular space by growing to larger sizes. This process results in morphologically asymmetric divisions, a finding that counters the long-assumed symmetry of E. coli cell division. In line with other recent evidence, our findings point to a more complex role of protein aggregation, with implications for our understanding of the cellular mechanisms underlying aging as well as its evolutionary origins.

evolutionary biology↗

bioRxiv2024

A link between aging and persistence

ABSRACTDespite the various strategies that microorganisms have evolved to resist antibiotic treatments, most chronic infections are caused by subpopulations of susceptible bacteria in a transient state of dormancy. This phenotype, known as bacterial persistence, arises due to a natural and ubiquitous heterogeneity of growth states in bacterial populations. Nonetheless, the unifying mechanism of persistence remains unknown, with several pathways being able to trigger the phenotype. Here, we show that asymmetric damage partitioning, a form of cellular aging, produces the underlying phenotypic heterogeneity upon which persistence is triggered. Using single-cell microscopy and microfluidic devices, we demonstrate that deterministic asymmetry in exponential phase populations leads to a state of growth stability, which prevents the spontaneous formation of persisters. However, as populations approach stationary phase, aging bacteria -- those inheriting more damage upon division -- exhibit a sharper growth rate decline, increased probability of growth arrest, and higher persistence rates. These results indicate that persistence triggers are biased by bacterial asymmetry, thus acting upon the deterministic heterogeneity produced by cellular aging. This work suggests unifying mechanisms for persistence and offers new perspectives on the treatment of recalcitrant infections. IMPORTANCEWhenever bacterial cultures are treated with antibiotics, a fraction of the population survives despite exhibiting no active resistance mechanisms. These "persisters" are cells in a state of slow growth or dormancy, already present in the population prior to antibiotic exposure. Although various stressors or mutations increase persistence rates, a unifying persistence mechanism has not been established. Here, we show that cellular aging can represent such a mechanism. Bacteria age through the inheritance of intracellular damage, which occurs even in unstressed populations. As populations approach stationary phase, aging Escherichia coli have a steeper decline in elongation rates and earlier division arrest compared to younger cells. Upon antibiotic treatment, aging bacteria have higher persistence rates. These results show that stationary phase, a well-established persistence trigger, operates on the phenotypic heterogeneity produced by cellular aging. Because aging is a deterministic and ubiquitous process, it could represent a fundamental mechanism for the formation of persisters.

evolutionary biology↗

bioRxiv2023

Declining old pole physiology gradually enhances gene expression asymmetry in bacteria

Gene expression is a heterogeneous process at the single-cell level. This heterogeneity is often coupled to individual growth rates, which are also highly stochastic, leading to the emergence of multiple physiological states within bacterial populations. Although recent advances have shown that cellular aging acts as a deterministic driver of growth asymmetry, the relationship between aging and gene expression heterogeneity remains elusive. Here we show that old poles undergo a progressive decline in gene expression as mother cells age, contributing to enhance phenotypic heterogeneity in bacterial populations. We quantified the activity of promoters with distinct activity profiles: a constitutive promoter, whose expression positively correlates with growth, and the promoter of RpoS, the general stress response sigma factor, for which growth and expression are mutually inhibitory. We demonstrate that mother cells have lower gene expression for both promoters. This asymmetry could not be explained by metabolic rate differences, but rather by the increasing intracellular heterogeneity of mother cells. As a mother ages, the declining activity of its old pole produces intracellular gradients in gene expression. This intracellular asymmetry manifests in the next generation as mother-daughter asymmetry, thus representing a source of phenotypic heterogeneity for the population. Our results show that bacterial asymmetry is built into the declining physiology of mother cells across generations, illustrating the deterministic nature of aging in bacterial systems. These findings provide further evidence for cellular aging as a mechanism to enhance the variance of metabolic states found in bacterial populations, with possible consequences for stress response and survival.

evolutionary biology↗