Biology subjects

Govers, S. K.

Publications and source records attributed to Govers, S. K..

7 recordsLinked to original sources

bioRxiv2025

Complex interplay between gene deletions and the environment uncovers cellular roles for genes of unknown function in Escherichia coli

Phenotypic outcomes can be heavily affected by environmental factors. In this study, we exploited the previously observed nutrient-dependency of cell biological phenotypic features, captured by a cross-condition image-based profiling assay of Escherichia coli deletion strains, to examine this in more detail. We identified several general principles, including the existence of a spectrum of deviating phenotypes across nutrient conditions (i.e., from nutrient- or feature-specific to pleiotropic phenotypic deviations), limited conservation of phenotypic deviations across nutrient conditions (i.e., limited phenotypic robustness), and a subset of nutrient-independent phenotypic deviations (indicative of consistent genetic determinants of specific phenotypic features). In a subsequent step, we used this cross-condition dataset to identify five genes of unknown function of which the deletion displayed either nutrient-independent phenotypic deviations or phenotypic similarities to genes of known function: yibN, yaaY, yfaQ, ybiJ, and yijD. These genes showed different levels of phylogenetic conservation, ranging from conserved across the tree of life (yibN) to only present in some genera of the Enterobacterales (yaaY). Analysis of the structural properties of the proteins encoded by these y-genes, identification of structural similarities to other proteins, and the examination of their subcellular localization yielded new insights into their contribution to E. coli cell morphogenesis, cell cycle progression and cell growth. Together, our approach showcases how bacterial image-based profiling assays and datasets can serve as a gateway to reveal the function of uncharacterized proteins. ImportanceDespite unprecedented access to genomic information, predicting phenotypes based on genotypes remains notoriously difficult. One major confounding factor is the environment and its ability to modulate phenotypic outcomes. Another is the fact that a large fraction of protein-coding genes in bacterial genomes remains uncharacterized and have no known function. In this work, we use a large-scale cross-condition image-based profiling dataset to characterize nutrient-dependent phenotypic variability of E. coli deletion strains and exploit it to provide insight into the cellular role of genes of unknown function. Through our analysis, we identified five genes of unknown function that we subsequently further characterized by examining their phylogenetic conservation, predicted structural properties and similarities, and their intracellular localization. Combined, this approach highlights the potential of cross-condition image-based profiling, which extracts many cell biological phenotypic readouts across multiple conditions, to better understand nutrient-dependent phenotypic variability and uncover protein function.

microbiology↗

bioRxiv2025

Large-scale genomic analysis reveals the distribution and diversity of Type VI Secretion Systems in Escherichia coli

The type VI secretion system (T6SS) is a versatile nanomachine that injects effectors into target cells, playing a role in bacterial competition and virulence. While widespread in Gram-negative bacteria, T6SS prevalence varies across species and strains, and its distribution in Escherichia coli remains underexplored despite E. coli being an important intestinal (IPEC) and extraintestinal (ExPEC) pathogen. Here, we examined the prevalence and distribution of T6SS subclasses (T6SSi) across 131610 E. coli genomes, which we annotated for clinical relevance. T6SS genes were identified while focusing on the three subclasses of T6SSi gene clusters known to be present in E. coli: T6SSi1, T6SSi2, and T6SSi4b. Across phylogenetic groups, T6SSi1 was broadly present, while T6SSi2 showed associations with B1, B2, and G, and T6SSi4b was rare. T6SSi1 was primarily associated with IPEC, and T6SSi2 with ExPEC. Even clearer patterns emerged at the sequence type (ST) level or when strains were further categorized into pathovars. For example, both the most dominant ExPEC and IPEC ST (ST131 and ST11, respectively) displayed niche-specific T6SS trends, with non-complete T6SSs being more associated with humans. In a final step, we evaluated the co-occurrence of T6SSs with other virulence-associated genes (VAGs) and multidrug resistance (MDR). This analysis confirmed the association of T6SSi1 and T6SSi2 with IPEC- and ExPEC-associated VAGs, respectively, and revealed a negative correlation between complete T6SSi subclasses and MDR. Together, our work provides a comprehensive overview of the diversity of T6SSs across E. coli, shedding more light on their potential contribution to pathogenicity in this species. ImportanceOur study represents a large-scale analysis of T6SSs across one of the most comprehensive collections of E. coli genomes to date. In doing so, we updated several misconceptions on T6SSs distribution and other genomic properties of E. coli strains, which originated from smaller scale studies and were subsequently extrapolated in the literature. This includes the prevalence and distribution of T6SSi subclasses across phylogenetic groups (e.g., T6SS i2 is not prevalent in phylogroup D), the association of specific virulence factors with IPEC and/or ExPEC (e.g., hemolysin A is more often associated with IPEC and not a typical ExPEC characteristic), and characteristics of pathogenic STs (e.g., ST131 displays distinct genomic properties based on its environmental niche). As such, this study not only advances our understanding of T6SS in E. coli, but also serves as a valuable resource for future studies on the clinical relevance and distribution of other genetic elements.

microbiology↗

bioRxiv2024

DNA/polysome phase separation and cell width confinement couple nucleoid segregation to cell growth in Escherichia coli

Chromosome segregation is essential for cellular proliferation. Unlike eukaryotes, bacteria lack cytoskeleton-based machinery to segregate their chromosomal DNA (nucleoid). The bacterial ParABS system segregates the duplicated chromosomal regions near the origin of replication. However, this function does not explain how bacterial cells partition the rest (bulk) of the chromosomal material. Furthermore, some bacteria, including Escherichia coli, lack a ParABS system. Yet, E. coli faithfully segregates nucleoids across various growth rates. Here, we provide theoretical and experimental evidence that polysome production during chromosomal gene expression helps compact, split, segregate, and position nucleoids in E. coli through out-of-equilibrium dynamics and polysome exclusion from the DNA meshwork, inherently coupling these processes to biomass growth across nutritional conditions. Halting chromosomal gene expression and thus polysome production immediately stops sister nucleoid migration while ensuing polysome depletion gradually reverses nucleoid segregation. Redirecting gene expression away from the chromosome and toward plasmids causes ectopic polysome accumulations that are sufficient to drive aberrant nucleoid dynamics. Cell width enlargement suggest that the proximity of the DNA to the membrane along the radial axis is important to limit the exchange of polysomes across DNA-free regions, ensuring nucleoid segregation along the cell length. Our findings suggest a self-organizing mechanism for coupling nucleoid segregation to cell growth.

microbiology↗

bioRxiv2023

The outer membrane and peptidoglycan layer form a single mechanical device balancing turgor

Bacteria are subject to a substantial concentration differential of osmolytes between the interior and exterior of the cell, which results in cytoplasmic turgor pressure. Failure to mechanically balance turgor pressure causes cells to burst. Here, we show that in Gram-negative bacteria, the outer membrane and peptidoglycan layer function together to resist turgor: when attached to each other, these two layers form a robust mechanical unit that allows pressure build-up in the periplasmic compartment, which in turn balances cytoplasmic turgor across the inner membrane, preventing cell death. Thus, the peptidoglycan layer is necessary but not sufficient to maintain turgor, which challenges the general view that protecting cells from bursting is the specific task of the peptidoglycan cell wall. ONE-SENTENCE SUMMARYThe peptidoglycan and outer membrane are interconnected layers that cooperate to balance cytoplasmic turgor.

microbiology↗

bioRxiv2023

Apparent simplicity and emergent robustness in bacterial cell cycle control

To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle and growth phenotypes of a fluorescently-labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often found to be nutrient-dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ-ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length). Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a systems-level understanding of the design principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability.

systems biology↗

bioRxiv2020

Chromosome dynamics and spatial organization during the non-binary cell cycle of a predatory bacterium

In bacteria, the dynamics of chromosome replication and segregation are tightly coordinated with cell cycle progression, and largely rely on specific spatiotemporal arrangement of the chromosome. Whereas these key processes are mostly investigated in species that divide by binary fission, they remain mysterious in bacteria producing larger number of descendants. Here, we establish the predatory bacterium Bdellovibrio bacteriovorus as a model to investigate the non-binary processing of a circular chromosome. Our data reveal its extreme compaction in a dense polarized nucleoid. We also show that a first binary-like cycle of replication and asymmetric segregation is followed by multiple asynchronous rounds of replication and progressive ParABS-dependent partitioning, uncoupled from cell division. Surprisingly, ParB localization at the centromere is cell-cycle regulated. Altogether, our findings support a model of complex chromosome choreography, leading to the generation of variable numbers of offspring, highlighting the adaptation of conserved mechanisms to achieve non-binary reproduction in bacteria.

microbiology↗

bioRxiv2018

Nucleoid size scaling and intracellular organization of translation across bacteria

The scaling of organelles with cell size is thought to be exclusive to eukaryotes. Here, we demonstrate that similar scaling relationships hold for the nucleoid in bacteria. Despite the absence of a nuclear membrane, nucleoid size strongly correlates with cell size, independent of changes in DNA amount and across various nutrient conditions. This correlation is observed in diverse bacteria, revealing a near-constant ratio between nucleoid and cell size for a given species. As in eukaryotes, the nucleocytoplasmic ratio in bacteria varies greatly among species. This spectrum of nucleocytoplasmic ratios is independent of genome size, and instead appears linked to the average cell size of the population. Bacteria with different nucleocytoplasmic ratios have different biophysical properties of the cytoplasm, impacting the mobility and localization of ribosomes. Together, our findings identify new organizational principles and biophysical features of bacterial cells, implicating the nucleocytoplasmic ratio and cell size as determinants of the intracellular organization of translation.

microbiology↗