Temporal order and precision of complex stress responses in individual bacteria

• Published in: Molecular systems biology Vol. 15; no. 2; pp. e8470 - n/a
• Main Authors: Mitosch, Karin, Rieckh, Georg, Bollenbach, Tobias
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-02-2019; EMBO Press; John Wiley and Sons Inc; Springer Nature
• Subjects: Anti-Bacterial Agents - pharmacology; Antibiotics; Bacteria; bacterial stress response; Biosynthesis; Cell division; Chains; Couplings; DNA damage; E coli; EMBO23; EMBO33; EMBO44; Escherichia coli - genetics; Fluorescence; Gene expression; Gene Expression Regulation, Bacterial - drug effects; Gene Expression Regulation, Bacterial - genetics; gene expression timing; Genomes; Kinetics; Metabolism; Microfluidics; Microfluidics - methods; Microscopy; Molecular chains; Nitrofurantoin; Oxidative stress; Oxidative Stress - drug effects; Oxidative Stress - genetics; Population; Promoters; Response time; Single-Cell Analysis - methods; single‐cell measurements; SOS response; SOS Response, Genetics - genetics; Standard deviation; Statistics; Stress response; Temporal variations; Trimethoprim; Upper bounds; Variability; single‐cell measurements; antibiotics; microfluidics; bacterial stress response; gene expression timing
• ISSN: 1744-4292; 1744-4292
• DOI: 10.15252/msb.20188470

Sudden stress often triggers diverse, temporally structured gene expression responses in microbes, but it is largely unknown how variable in time such responses are and if genes respond in the same temporal order in every single cell. Here, we quantified timing variability of individual promoters responding to sublethal antibiotic stress using fluorescent reporters, microfluidics, and time‐lapse microscopy. We identified lower and upper bounds that put definite constraints on timing variability, which varies strongly among promoters and conditions. Timing variability can be interpreted using results from statistical kinetics, which enable us to estimate the number of rate‐limiting molecular steps underlying different responses. We found that just a few critical steps control some responses while others rely on dozens of steps. To probe connections between different stress responses, we then tracked the temporal order and response time correlations of promoter pairs in individual cells. Our results support that, when bacteria are exposed to the antibiotic nitrofurantoin, the ensuing oxidative stress and SOS responses are part of the same causal chain of molecular events. In contrast, under trimethoprim, the acid stress response and the SOS response are part of different chains of events running in parallel. Our approach reveals fundamental constraints on gene expression timing and provides new insights into the molecular events that underlie the timing of stress responses.
Synopsis
Single‐cell measurements of individual promoter timing variability and the temporal order of gene expression in response to antibiotic stress in
Escherichia coli
reveal connections between promoters and provide a detailed view into the temporal organization of stress responses.
Cell‐cell variability in the timing of gene expression is quantified for dozens of
E. coli
promoters upon sudden exposure to different antibiotics.
Timing variability increases with response time and has clear lower and upper bounds, which are interpreted using statistical kinetics.
A dual‐reporter approach reveals the temporal order of responses at the single‐cell level, corroborating or refuting mechanistic couplings between different cellular response systems.
Graphical Abstract
Single‐cell measurements of individual promoter timing variability and the temporal order of gene expression in response to antibiotic stress in
Escherichia coli
reveal connections between promoters and provide a detailed view into the temporal organization of stress responses.