Research

Rahul Jagadeesan, Suchintak Dash, Cristina S. D. Palma, Ines S. C. Baptista, Vatsala Chauhan, Jarno Mäkelä, Andre S. Ribeiro (2025) Sci. Adv. 11, eadl3570.

DOI: 10.1126/sciadv.adl3570

Data: https://datadryad.org/dataset/doi:10.5061/dryad.zgmsbccks

Bacterial gene networks have operons, each coordinating several genes under a primary promoter. Half of the operons in Escherichia coli have been reported to also contain internal promoters. We studied their role during genome-wide stresses targeting key transcription regulators, RNA polymerase (RNAP) and gyrase. Our results suggest that operons’ responses are influenced by stress-related changes in premature elongation terminations and internal promoters’ activity. Globally, this causes the responses of genes in the same operon to differ with the distance between them in a wave-like pattern. Meanwhile, premature terminations are affected by positive supercoiling buildup, collisions between elongating and promoter-bound RNAPs, and local regulatory elements. We report similar findings in E. coli under other stresses and in evolutionarily distant bacteria B subtilis, C glutamicum, and H pylori. Our results suggest that the strength, number, and positioning of operons’ internal promoters might have evolved to compensate for premature terminations, providing distal genes similar response strengths.

Baptista ISC, Dash S, Arsh AM, Kandavalli V, Scandolo CM, Sanders BC, and Ribeiro AS (2025) Bimodality in E. coli gene expression: Sources and robustness to genome-wide stresses. PLoS Comput Biol 21(2): e1012817. 

https://doi.org/10.1371/journal.pcbi.1012817

Data Availability: https://doi.org/10.5061/dryad.dz08kps5n;

Software: https://doi.org/10.5281/zenodo.14746159;

Supplemental information: https://doi.org/10.5281/zenodo.14746189.

Bacterial cell populations exhibiting multiple phenotypes under the same environmental condition should have enhanced survival chances to unpredictable environmental fluctuations. This capacity could rely on genes with the ability to switch between high- and low-expression levels, under the same environment. So far, few genes are known to have such a capacity. We report on seven genes with bimodal dynamics, show that bimodality is robust to some but not all stresses, and reversibility of bimodality if returning to control conditions. We also show evidence that bimodality emerges from events in transcription initiation and propose a model of their behavior. Our findings could advance research on bacterial decision-making processes and engineering multi-stable synthetic circuits.

Escherichia coli have evolved hundreds of transcription factors to tune the expression of thousands of genes. Interestingly, a few transcription factors control almost half of all genes and are thus named global regulators (GRs). Tracking the numbers of these GRs over time is essential to understand phenotypic modifications, e.g., under stress conditions. We have engineered a library of strains to track GR levels. Each strain has a single-copy plasmid coding for a fast-maturing green fluorescent protein whose transcription is controlled by a copy of the natural promoter of the GR. This library should become useful in scientific research, and future applications in therapeutics and the bioindustries. For more information, please visit: 10.1128/msystems.00065-24.

Bacteria process information to bind past events to future actions, so as to adapt to environment changes. This is made possible by a timely organized execution of multiple tasks such as counting time, sensing the environment, and decision making, which are performed in parallel, by semi-independent, tuned small genetic circuits. These circuits differ in structure, which defines the function. Meanwhile, the properties of their internal components, e.g. the kinetics of transcription initiation of the promoters, define the efficiency with how functions are performed.

We constructed a single-copy repressilator (SCR) by implementing the original repressilator circuit of Elowitz et al on a single-copy F-plasmid. We studied its behaviour as a function of temperature and compared to the original low-copy-number repressilator (LCR). In optimal temperature, the dynamics of the two systems differ, but respond similarly to temperature changes. Interestingly, the SCR is more robust to lower temperatures and perturbations than the original LCR, which loses functionality as temperature increases beyond 30 C, due to the loss of functionality of one of its proteins, CI.

Z-rings and Cell Division

Cell division in E coli is morphologically symmetric due to, among other, their ability to place the Z-ring at midcell. At sub-optimal temperatures, this symmetry decreases at the single-cell level. Using fluorescence microscopy, we observed FtsZ-GFP and DAPI-stained nucleoids to assess the robustness of the symmetry of Z-ring formation and positioning in cells at sub-optimal and critical temperatures. We found that the Z-ring formation and positioning is robust at sub-optimal temperatures, as the Z-ring ’ s mean width, density and displacement from midcell maintain correlation to one another. However, at critical temperatures, the Z-ring displacement from midcell is greatly increased. This is due to enhanced distance between the replicated nucleoids and, thus, reduced Z-ring density, which explains the weaker precision in setting a morphologically symmetric division site. This also occurs in rich media and is cumulative, i.e. combining richer media and critically high temperatures enhances the asymmetries in division, which is evidence that the causes are biophysical. To support this, we showed that the effects are reversible, i.e. shifting cells from optimal to critical, and then to optimal again, reduces and then enhances the symmetry in Z-ring positioning, respectively. Overall, we found that Z-ring positioning in E. coli is a robust biophysical process under sub-optimal temperatures, and that critical temperatures cause significant asymmetries in division.