In recent years, the phenomenon of liquid–liquid phase separation and the formation of membraneless organelles have revolutionized our understanding of intracellular organization. While eukaryotic cells are known to harbor liquid droplets that serve as dynamic hubs for RNA processing and storage, the occurrence and role of analogous structures in prokaryotes have remained enigmatic. Now, pioneering research spearheaded by Pei, L., Xian, Y., Yan, X., and colleagues has uncovered compelling evidence that Escherichia coli employs aggresome-like condensates to sequester messenger RNA (mRNA) during prolonged stress, significantly enhancing bacterial survival and recovery. Published in Nature Microbiology, this study elucidates the physicochemical properties, molecular composition, and biological functions of these hitherto overlooked ribonucleoprotein assemblies in bacteria, pointing to an evolutionarily conserved strategy for post-transcriptional regulation.
The crux of the investigation centers on aggresomes, intracellular proteinaceous condensates traditionally associated with the sequestration of misfolded proteins. By deploying sophisticated live-cell imaging techniques combined with polymer physics modeling, the team demonstrated that these aggresomes undergo pronounced formation and compaction under conditions of cellular stress characterized by ATP depletion. This metabolic constraint—commonplace in nutrient-poor or hostile environments—provokes a phase transition that consolidates specific mRNA subsets into dense, membraneless droplets. Notably, these findings imply that beyond their canonical function in protein quality control, aggresomes in E. coli serve as specialized storage compartments for mRNA, preserving the transcriptome’s integrity in challenging milieus.
In-depth analyses revealed a striking enrichment of longer mRNA transcripts within the aggresomes compared to the surrounding cytosol. This preferential accumulation is indicative of a selective sequestration mechanism, potentially governed by transcript length and sequence-dependent physicochemical properties. Such differential partitioning might be instrumental in prioritizing the preservation of transcripts encoding proteins critical for post-stress recovery, thereby optimizing the bacterium’s regeneration strategy after environmental insults are relieved. The implications extend to the broader understanding of bacterial gene expression dynamics, suggesting spatial regulation of mRNA availability as a previously underappreciated facet of stress responses.
Central to the protective nature of these aggresomes is the exclusion of mRNA-degrading enzymes such as ribonucleases. Through targeted mass spectrometry and mutagenesis experiments, the research team showed that the surface charges of ribonucleases confer electrostatic repulsion, effectively barring their entry into the negatively charged aggresome matrix. This selective barrier ensures that stored transcripts evade enzymatic degradation, facilitating mRNA stabilization during protracted periods of stress. The detailed biophysical rationale underpinning this exclusion phenomenon enriches the conceptual framework of cellular compartmentalization absent classical membrane boundaries.
The functional consequences of mRNA storage within aggresomes were underscored by experiments utilizing fluorescent reporter constructs. By enabling real-time monitoring of translation dynamics post-stress, these assays demonstrated accelerated resumption of protein synthesis from stored transcripts once normal conditions were restored. Correspondingly, bacteria exhibiting robust aggresome formation displayed truncated lag phases and enhanced growth rates during recovery, correlating molecular sequestration events with population-level fitness gains. This remarkable adaptive advantage positions aggresomes as central players fostering bacterial resilience amidst fluctuating environments.
From a methodological standpoint, the multidisciplinary approach adopted by Pei and colleagues is noteworthy. Polymer physics modeling offered quantitative insights into the mechanics of phase separation and transcript compaction within aggresomes, bridging molecular observations with theoretical frameworks. The marriage of cutting-edge imaging modalities, including high-resolution live-cell microscopy, with comprehensive transcriptomic profiling enabled a nuanced mapping of mRNA landscapes in stressed versus non-stressed cells. Such integration of diverse techniques sets a new benchmark for investigations into membraneless organelles in prokaryotes.
These discoveries challenge long-standing paradigms that have largely confined the concept of phase-separated RNA granules to eukaryotic contexts. By demonstrating that bacteria not only form analogous condensates but adeptly exploit them for mRNA preservation and translational control, this study extends the evolutionary footprint of cellular compartmentalization strategies. It invites reevaluation of bacterial physiology, particularly under stress, and may spur renewed interest in exploring phase separation phenomena across diverse microbial taxa.
Beyond fundamental biology, the implications of bacterial aggresomes for biotechnology and medicine are substantial. Understanding how pathogens preserve transcripts during host-imposed stresses could inform the development of novel antimicrobial interventions that disrupt these protective condensates, thereby sensitizing bacteria to immune clearance or antibiotic attack. Similarly, harnessing aggresome-like systems might enhance synthetic biology applications by stabilizing mRNA populations in engineered microbes, improving their robustness under industrial conditions.
The study’s revelations also contribute to the broader dialogue on RNA metabolism and regulation. Previously, mRNA degradation and translation were viewed predominantly as cytosolic events governed by diffusible factors. The discovery that mRNA can be spatially sequestered in phase-separated compartments introduces an additional regulatory dimension, where transcript stability and availability are modulated by physical segregation. This paradigm shift should stimulate further research into mRNA localization patterns, their determinants, and functional consequences within bacterial cells.
Moreover, the electrostatic principles governing ribonuclease exclusion from aggresomes underscore the significance of physicochemical microenvironments in shaping molecular interactions. This points to an elegant mechanism whereby bacteria leverage intrinsic biophysical properties to engineer selective permeability barriers sans lipid membranes. Deciphering these rules will enrich the understanding of how cells orchestrate biochemical processes within crowded, heterogeneous interiors.
Looking ahead, several open questions remain to be addressed. For instance, what molecular determinants steer specific mRNAs into the aggresomes? Are there accessory proteins or RNA-binding factors guiding this recruitment? How reversible is aggresome formation, and what signals mediate the release of stored transcripts? Delineating these mechanistic aspects will deepen insight into bacterial stress responses and may uncover new regulatory nodes amenable to manipulation.
Additionally, it will be intriguing to explore whether similar aggresome-like structures exist across other bacterial species or domains of life, providing clues about the universality of liquid–liquid phase separation as an adaptive tool. Cross-species comparisons could also reveal evolutionary adaptations linking aggresome composition and function to environmental niches or lifestyle strategies.
Taken together, this pioneering investigation illuminates a novel facet of bacterial cell biology, revealing how E. coli harnesses aggresomes to protect mRNA from degradation under stress and reinitiate translation swiftly upon recovery. This discovery enriches our conceptual repertoire of intracellular compartmentalization, highlighting membraneless organelles as vital agents sustaining bacterial viability in adversity. By integrating biophysical principles, molecular biology, and imaging, Pei, L. and colleagues establish a compelling narrative that poised to redefine bacterial stress adaptation frameworks and inspire diverse future research avenues.
Subject of Research: mRNA dynamics and storage within membraneless aggresome condensates during stress in Escherichia coli
Article Title: Aggresomes protect mRNA under stress in Escherichia coli
Article References:
Pei, L., Xian, Y., Yan, X. et al. Aggresomes protect mRNA under stress in Escherichia coli. Nat Microbiol (2025). https://doi.org/10.1038/s41564-025-02086-5
Image Credits: AI Generated
