Molecular Time Sharing through Dynamic Pulsing in Single Cells

Abstract

SUMMARY In cells, specific regulators often compete for limited amounts of a core enzymatic resource. It is typically assumed that competition leads to partitioning of core enzyme molecules among regulators at constant levels. Alternatively, however, different regulatory species could time share, or take turns utilizing, the core resource. Using quantitative time-lapse microscopy, we analyzed sigma factor activity dynamics, and their competition for RNA polymerase, in individual Bacillus subtilis cells under energy stress. Multiple alternative sigma factors were activated in ~1-hr pulses in stochastic and repetitive fashion. Pairwise analysis revealed that two sigma factors rarely pulse simultaneously and that some pairs are anti-correlated, indicating that RNAP utilization alternates among different sigma factors. Mathematical modeling revealed how stochastic time-sharing dynamics can emerge from pulse-generating sigma factor regulatory circuits actively competing for RNAP. Time sharing provides a mechanism for cells to dynamically control the distribution of cell states within a population. Since core molecular components are limiting in many other systems, time sharing may represent a general mode of regulation.

Microbial single-cell RNA sequencing by split-pool barcoding

“…Additionally, we found that correlations between the sigma factor regulons largely agreed with the concept of molecular time sharing, i.e. the idea that sigma factors compete for RNA polymerases (Figure S7) (22).…”

“…To obtain an even finer-grained picture of the transcriptional programs during exponential growth and entry to stationary phase, we inferred the activity profiles of select transcriptional regulators (TR) from expression of the genes in their respective regulons (Figure 2D and S8) (22). This analysis revealed pronounced changes in regulation of carbon utilization, stress responses, metal uptake, developmental decisions and more.…”

Preexisting variation in DNA damage response predicts the fate of single mycobacteria under stress

“…The EMBO Journal 38: e101876 | 2019 associated with transient fitness gain (Smits et al, 2006;Veening et al, 2008). For instance, in Bacillus subtilis alternative sigma factors are expressed in pulses (Park et al, 2018), likewise the tumor suppressor p53 in eukaryotic cells (Lahav et al, 2004). In E. coli, the DNA repair methyltransferase Ada is heterogeneously expressed in stress-free populations, also conferring discrete responsiveness to alkylating agents (Uphoff et al, 2016).…”

Escherichia colican survive stress by noisy growth modulation

“…Gene expression can be noisy 1,2 , as can the growth of single cells 3,4 . Such cell-to-cell variation has been implicated in survival strategies for bacterial populations 5–7 .…”

“…3d, 4b). However, the ΔrpoS strain also had a wide growth rate distribution suggesting growth rate is intrinsically heterogeneous 3 (Fig. 2e).…”