Biology subjects

Sassi, A. S.

Publications and source records attributed to Sassi, A. S..

3 recordsLinked to original sources

bioRxiv2026

Ultrasensitive response in bacterial replication initiation

In bacteria, the time at which genome replication initiates is carefully regulated, as precision in this timing is crucial for cell cycle stability. Theoretical and experimental studies have shown that the probability of replication initiation sharply depends on cell volume as the cell grows. Such sharp response is usually termed "ultrasensitive" in biology, and has been subject of extensive theoretical study. Nevertheless, the source of ultrasensitivity in this system remains unclear. In this work, we show how ultrasensitivity in replication initiation emerges from the dynamics of DnaA, the central protein regulating initiation in all bacterial species. To do so, we propose a mechanistic, thermodynamically consistent model of the dynamics of DnaA, and study the conditions under which an ultrasensitive response arises. We find that ultrasensitivity results from a combination of regulatory processes, that varies with growth conditions. In slow growth, we find an interplay between sequestration of DnaA on chromosomal binding sites and DnaA binding at the origin of replication. This mechanism requires a "sweet spot" of origin binding affinities, whose values are consistent with available experimental measurements. In fast growth, ultrasensitivity instead arises from rapid transition between an inactive and an active form of DnaA, and requires cooperative binding at the origin of replication to be effective. Our results point to ultrasensitivity as the organizing principle underlying regulation of bacterial replication initiation.

systems biology↗

bioRxiv2021

A multi-state dynamical process underpins mechano-adaptation in the bacterial flagellar motor

Adaptation is a defining feature of living systems. The bacterial flagellar motor adapts to changes in the external mechanical environment by adding or removing torque-generating stator units. However, the molecular mechanism for mechanosensitive motor remodeling remains unclear. Here, we induced stator disassembly using electrorotation, followed by the time-dependent assembly of the individual stator units into the motor after electrorotation was terminated. From these experiments, we extracted detailed statistics of the dwell times that comprise the stochastic dynamics of the binding and unbinding of stator units. Dwell times reveal multiple timescales, indicating the existence of multiple binding states of the stator units. Based on these results, we propose a minimal model in which the stator unit can occupy four different states - two bound states with very different rates of unbinding, a diffusive unbound state, and a transiently detached state. Our minimal model quantitatively explains multiple features of the experimental data and allows us to determine the transition rates among all four states. Our experiments and modeling suggest a mechanism of mechano-adaptive remodeling of the bacterial flagellar motor in which torque generated by bound stator units controls their effective unbinding rate by modulating the transition between the two bound states. Furthermore, the binding rate of stator units with the motor has a non-monotonic dependence on the number of bound units, likely because of two counteracting effects of motor rotation on the binding process.

biophysics↗

bioRxiv2020

A filter-and-integrate mechanism generates stochastictranscriptional pulses in E.coli flagellar synthesis

Stochastic pulsatile dynamics have been observed in an increasing number of biological circuits with typical mechanism involving feedback control. Surprisingly, recent single-cell experiments showed that E. coli flagellar class-2&3 promoters are activated in stochastic pulses without the means of feedback, however, the underlying design principles of pulse generation have remained unclear. Here, by developing a system-level stochastic model constrained by a large set of E. coli flagellar synthesis data from different strains and mutants, we identify the underlying design principles for generating stochastic transcriptional pulses without feedback. Our model shows that YdiV, an inhibitor of the class-1 master regulator (FlhDC), creates an ultrasensitve switch that serves as a digital filter to eliminate small amplitude FlhDC fluctuations. Additionally, we demonstrate that fast temporal fluctuations of FlhDC are smoothed out and integrated over time before affecting class-2 downstream genes. Together, our results reveal the existence of a filter-and-integrate design that is necessary for generating stochastic pulses without feedback. This strategy suggests that E. coli may avoid premature activation of the expensive flagellar gene expression by filtering input fluctuations in intensity and in time.

microbiology↗