Biology subjects

Goulev, Y.

Publications and source records attributed to Goulev, Y..

4 recordsLinked to original sources

bioRxiv2026

Division of labor during bacterial warfare

Division of labor is commonly associated with cooperative behavior, yet one of its most extreme forms occurs during bacterial warfare, where a subset of cells undergoes suicidal lysis to release toxins. Why bacteria divide labor among a few cells rather than producing toxin uniformly remains unknown. Here, we combine timelapse microscopy and simulations, to understand the division of labor during bacterial warfare using bacteriocin (colicin) production by the gut bacterium Escherichia coli as a model system. At the single-cell level, we find that lytic toxin production is a tightly regulated event: only cells that commit to lysis produce significant toxin and then lysis only occurs once a large amount of toxin has been made. This high threshold ensures each sacrifice delivers a large dose, which is released in a rapid burst from a lysing cell. While such burst-like release appears to provide no advantage over uniform labor in well-mixed conditions, we show it becomes extremely effective in spatially structured populations where the rapid release of toxin by one cell can generate lethal concentrations locally and eliminate competitors. Finally, we explain why the lysing fraction remains so small. While an increase in the producing cells increases toxin levels, it also increases the probability of local patch extinctions. The division of labor during bacterial warfare, therefore, enables powerful localized killing while safeguarding the population from self-destruction.

microbiology↗

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↗

bioRxiv2025

Essentialome-Wide Multigenerational Imaging Reveals Mechanistic Origins of Cell Growth Laws

Escherichia coli is arguably the most thoroughly characterized organism, and yet [~]20% of its essential genes serve completely unknown functions,1,2 and many core quantitative physiological principles remain unexplained, including the famous nutrient growth law where cell volume seems to depend exponentially on growth rate. Here we develop a platform for massive, multi-generational Optical Pooled Screening (OPS)3-6, and apply it to link image-based phenotypes to genotypes for 133,000 CRISPRi knockdowns of essential genes, tracking tens of millions of lineages and analyzing 1.6 billion cells. Our multi-dimensional dynamic phenotypes correlate exceptionally well with known gene functions, allowing us to identify many unknown roles of essential genes. Quantifying the relation between growth and cell size in turn identifies three distinct variants of the bacterial growth laws, which we explain mechanistically by discovering a new role for (p)ppGpp and SpoT as a sensor of translation elongation. Finally, we propose and systematically test an exceedingly simple, passive mechanism for the nutrient growth law, based on triggering cell division through the accumulation of a protein that, unlike ribosomes, is not controlled by (p)ppGpp. The resulting hyperbolic growth law fits the data from our three variants even better than the previously proposed exponential relationship, and with fewer parameters.

systems biology↗

bioRxiv2019

COSPLAY: An expandable toolbox for combinatorial and swift generation of expression plasmids in yeast

A large number of genetic studies in yeast rely on the use of expression vectors. To facilitate the experimental approach of these studies, several collections of expression vectors have been generated (YXplac, pRS series, etc.). Subsequently, these collections have been expanded by adding more diversity to many of the plasmid features, including new selection markers and new promoter sequences. However, the ever growing number of plasmid feature makes it unrealistic for research labs to maintain an up-to-date collection of plasmids.. Here, we developed the COSPLAY toolbox: a Golden Gate approach based on the scheme of a simple modular plasmid that recapitulates and completes all the properties of the pRS plasmids. The COSPLAY toolbox contains a basal collection of individual functional modules. Moreover we standardized a simple and rapid, software-assisted protocol which facilitates the addition of new personalized modules. Finally, our toolbox includes the possibility to select a genomic target location and to perform a single copy integration of the expression vector.

molecular biology↗