Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit

Abstract

Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σ V circuit in Bacillus subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σ V under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.

Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions

“…The mother machine device is popular for studies of cellular heterogeneity because the environmental conditions are believed to be so uniform that any phenotypic variation can be attributed to intracellular noise sources. 18 , 45 , 50 , 51 However, this assumption is rarely tested rigorously. Here, we noticed that cells at the open end of the trenches exhibited higher OxyR reporter expression compared with cells located at the closed end during H 2 O 2 treatment ( Figures 1 A, 1B, and 1D; Video S1 ).…”

Microfluidics for long-term single-cell time-lapse microscopy: Advances and applications

“…Molecular “time-sharing” was proposed as a mechanism in which alternative sigma factors competing for RNA polymerase binding opportunities are able to share such core resources over time ( Park et al, 2018 ). Stochastic bursts of sigma factor activity also seem to play a role in stress response in B. subtilis : heterogeneous response to lysozyme stress was observed between individual cells grown in the MM ( Schwall et al, 2021 ). Pulsatile expression of the sigV operon preceding exposure to lysozyme stress led to increased survival probability.…”

VariableDNAtopology is an epigenetic generator of physiological heterogeneity in bacterial populations

“…Precise synchronization of these transcription patterns across every cell in the population is impossible, resulting in cell‐to‐cell variations in the outputs from copies of the same genes in different cells. Transcriptional activity is modulated not only by the genome‐wide distribution of RNA polymerase and the topoisomerases, but also by the actions of, inter alia, transcription factors, nucleoid‐associated proteins, sigma factors, intrinsic and extrinsic transcription terminators, and by the stalling and backtracking of RNA polymerase (Figueroa‐Bossi et al, 2022 ; Janissen et al, 2022 ; Schwall et al, 2021 ). This produces a population of cells exhibiting transcription patterns that are noisy and randomized (Urchueguía et al, 2021 ).…”