Biology subjects

Laganenka, L.

Publications and source records attributed to Laganenka, L..

6 recordsLinked to original sources

bioRxiv2026

Autoinducer-2 functions as both a quorum sensing and metabolic signal in Escherichia coli

Bacteria integrate diverse environmental signals to coordinate behavior, yet the relationship between nutrient sensing and quorum sensing (QS) remains incompletely understood. Autoinducer-2 (AI-2) is unique among QS signals in that its production is tightly linked to central metabolism, raising fundamental questions about the boundary between metabolic and signaling functions. In Escherichia coli, AI-2 coordinates collective behaviors through the lsr operon, whose expression is controlled not only by the AI-2-responsive repressor LsrR but also by the cAMP receptor protein (CRP), placing it at the intersection of carbon sensing and population-level signaling. While inhibition of lsr operon expression by PTS sugars such as glucose was previously established, we demonstrate that non-PTS sugars similarly suppress lsr expression through CRP, further decoupling QS activation from cell density and coupling it to carbon source availability. Systematic analysis of Enterobacteriaceae genomes reveals that CRP binding sites in the lsr promoter region are broadly conserved, indicating that metabolic modulation of AI-2 signaling is an ancestral regulatory feature. Importantly, using a FRET-based biosensor, we show that AI-2 uptake modulates intracellular cAMP levels in a manner resembling non-PTS carbon source transport, suggesting that AI-2 may have originally functioned as a nutrient substrate, with its signaling role emerging subsequently or co-evolving alongside. In support of this hypothesis, we isolated soil- and phyllosphere-associated bacteria capable of utilizing AI-2 as a sole carbon source. Our findings reveal an underappreciated metabolic dimension of AI-2 QS and suggest an evolutionary trajectory in which AI-2 signaling emerged from ancestral carbon utilization pathways. ImportanceQS allows bacteria to coordinate collective behaviors by detecting secreted signaling molecules, yet the evolutionary origins of these systems remain poorly understood. AI-2, one of the most broadly conserved bacterial signals, is derived from central metabolism and processed by machinery in E. coli that strikingly resembles a sugar utilization system. Here, we show that nutrient availability overrides cell density as the primary determinant of AI-2 responsiveness, that this regulatory logic is conserved among Enterobacteriaceae genomes, and that environmental bacteria can grow on AI-2 as a sole carbon source. These findings reframe AI-2 as a signal embedded within, and potentially evolved from, nutrient sensing pathways, with direct implications for understanding how byproducts of cellular metabolism can acquire signaling functions.

microbiology↗

bioRxiv2025

Emergent spatial structure in the gut microbiota is driven by bacterial growth and gut contractions

Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters of the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. In samples from mice and humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid that changes its viscoelastic properties under the force of gut contractions. This phenomenon is sufficient to explain micro-scale bacterial clustering in the murine cecum, resulting from growth within the gel-like structure of cecum content, and periodic disruption due to peristalsis-driven shear-thinning and clearance. Shear-thinning can also explain the surprising observation that fed beads enter the tip of the mouse cecum by flow along the epithelial cell layer before being mixed into the cecum content. Our study shows mechanistically how spatial structure in the gut emerges through the interplay of microbial and host physiology and highlights the possibility of host control over gut microbiota distribution via gut contractions. One sentence summaryWe show how spatial structure emerges in the gut microbiota through bacterial growth in the matrix of gut content.

systems biology↗

bioRxiv2025

The Gfr uptake system provides a context-dependent fitness advantage to Salmonella Typhimurium SL1344 during the initial gut colonization phase

Salmonella enterica serovar Typhimurium (S. Tm) is a major cause of foodborne diarrhea. However, in healthy individuals, the microbiota typically restricts the growth of incoming pathogens, a protective mechanism termed colonization resistance (CR). To circumvent CR, Salmonella strains can utilize private nutrients that remain untapped by the resident microbiota. However, the metabolic pathways and environmental niches promoting pathogen growth are still not completely understood. Here, we investigate the significance of the gfr operon in gut colonization of S. Tm, which is essential for the utilization of fructoselysine (FL) and glucoselysine (GL). These Amadori compounds are present in heated foods with high protein and carbohydrate contents, particularly in Western-type diets. We detected FL in both mouse chow and the intestinal tract of mice and showed that gfr mutants are attenuated during the initial phase of colonization in the murine model. Experiments in gnotobiotic mice and competition experiments with Escherichia coli suggest that gfr-dependent fitness advantage is context-dependent. We conclude that dietary Amadori products like FL can support S. Tm gut colonization, depending on the metabolic capacities of the microbiota.

microbiology↗

bioRxiv2025

Strain-specific galactose utilization by commensal E. coli mitigates Salmonella establishment in the gut

Salmonella enterica serovar Typhimurium (S. Tm) is a major cause of gastrointestinal diseases worldwide. To date, options for prevention or curative therapy remain limited. The gut microbiota plays a protective role against enteric diseases, particularly in preventing establishment and proliferation of S. Tm. While most research has focused on microbiota-mediated pathogen exclusion during the later, inflammation-dominated stages of infection, little is known about how microbiota members mitigate S. Tm early gut colonization. To address this gap, we conducted 24 h in vivo competitive experiments using S. Tm and different commensal E. coli strains. We observed a significant reduction in pathogen load, which was strain-specific and particularly evident with E. coli 8178. To investigate the underlying molecular mechanisms, we performed an in vivo screen using a rationally designed S. Tm library -which includes a wide range of carbohydrate utilization mutants - both in the absence and presence of E. coli strains. Our findings revealed that E. coli 8178-mediated S. Tm competition was driven by the exploitation of galactose during the early stage of infection. Identifying galactose as a key metabolite in pathogen exclusion by gut microbiota members enhances our mechanistic understanding of microbiota-mediated protection and opens new avenues for developing microbiota- and dietary-based strategies to better control intestinal infections.

microbiology↗

bioRxiv2024

Interplay between chemotaxis, quorum sensing, and metabolism regulates Escherichia coli-Salmonella Typhimurium interactions in vivo

Motile bacteria use chemotaxis to navigate complex environments like the mammalian gut. These bacteria sense a range of chemoeffector molecules, which can either be of nutritional value or provide a cue for the niche best suited for their survival and growth. One such cue molecule is the intra- and interspecies quorum sensing signaling molecule, autoinducer-2 (AI-2). Apart from controlling collective behavior of Escherichia coli, chemotaxis towards AI-2 contributes to its ability to colonize the murine gut. However, the impact of AI-2-dependent niche occupation by E. coli on interspecies interactions in vivo is not fully understood. Here, using the C57BL/6J mouse infection model, we show that chemotaxis towards AI-2 contributes to nutrient competition and thereby affects colonization resistance conferred by E. coli against the enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm). Like E. coli, S. Tm also relies on chemotaxis, albeit not towards AI-2, to compete against residing E. coli in a gut inflammation-dependent manner. Finally, by using a barcoded mutant library pool of S. Tm, we analyzed how AI-2 signaling in E. coli affects the central metabolism of S. Tm. AI-2-dependent niche colonization by E. coli specifically affected the fitness of S. Tm mutants deficient in fumarate respiration ({Delta}dcuABC) or mannose ({Delta}manA) utilization. Our findings thus provide important insights into AI-2-mediated E. coli-S. Tm interactions during gut infection. Author SummaryBoth chemotaxis and AI-2 quorum sensing systems have been extensively studied in Escherichia coli. Despite our understanding of these systems at a molecular level in vitro, their physiological relevance in vivo, particularly in the context of mammalian gut colonization, remains less explored. Building on our previous work on the role of chemotaxis and AI-2 signaling in E. coli gut colonization, we investigated their roles in interspecies interactions. Specifically, we examined how AI-2-dependent colonization by E. coli affects its competition with the enteric pathogen Salmonella enterica serovar Typhimurium (S. Tm) and the metabolic requirements for S. Tm growth. Our data show that AI-2 signaling contributes to colonization resistance of E. coli against S. Tm. Although S. Tm also requires chemotaxis to grow efficiently in E. coli-colonized mice, this is independent of its ability to sense AI-2. Notably, AI-2-dependent niche occupation by E. coli altered S. Tm metabolism at different stages of infection. Collectively, our findings highlight how AI-2 signaling in one species can affect the metabolism of its interaction partners in vivo.

microbiology↗

bioRxiv2022

The mobilizable plasmid P3 of Salmonella enterica serovar Typhimurium SL1344 depends on the P2 plasmid for conjugative transfer into a broad range of bacteria in vitro and in vivo

The global rise of drug-resistant bacteria is of great concern. Conjugative transfer of antibiotic resistance plasmids contributes to this antibiotic resistance crisis. Despite the substantial progress in understanding the molecular basis of conjugation in vitro, the in vivo dynamics of intra- and interspecies conjugative plasmid transfer are much less understood. In this study, we focused on the streptomycin resistance-encoding mobilizable plasmid pRSF1010SL1344 (P3) of Salmonella enterica serovar Typhimurium (S. Tm) strain SL1344. We show that P3 is mobilized by interacting with the conjugation machinery of a second, conjugative plasmid pCol1B9SL1344 (P2) of SL1344. Thereby, P3 can be transferred into a broad range of relevant environmental and clinical bacterial isolates in vitro and in vivo. Our data suggests that S. Tm persisters in host tissues can serve as P3 reservoirs and foster transfer of both, P2 and P3 once they reseed the gut lumen. This adds to our understanding of resistance plasmid transfer in ecologically relevant niches including the mammalian gut. IMPORTANCES. Tm is a remarkably adaptable and globally abundant bacterial species that rapidly occupies new niches and survives unstable environmental conditions. As an enteric pathogen, it can potentially interact with a broad range of bacterial species residing in the mammalian gut. High abundance of bacteria in the gut lumen facilitate conjugation and spread of plasmid-encoded antibiotic resistance genes. By studying the transfer dynamics of the P3 plasmid in vitro and in vivo, we illustrate the impact of S. Tm-mediated antibiotic resistance spread via conjugation to a variety of relevant environmental and clinical bacterial isolates. Along with temperate phages or naked DNA, plasmids are among the most critical vehicles driving antibiotic resistance spread. Further understanding of the dynamics and drivers of antibiotic resistance transfer, along with identifying the environmental niches where this occurs, is needed to develop effective solutions for slowing down the emerging threat of multidrug-resistant bacterial pathogens.

microbiology↗