Transient transcription factor depletions explain diverse single-cell responses of LexA target promoters to mild DNA damage

Abstract

In bacteria, the effects of transcription factors (TFs) on the expression of their target genes are highly stochastic at the single-cell level. Not only do TF concentrations fluctuate in time and from cell to cell, in each cell the actual binding and unbinding of TFs to promoters is also stochastic. However, how this noise propagation from TFs to their targets determines the expression fluctuations in target genes of the same TF has so far not been quantitatively characterized. Here we use fluorescence time-lapse microscopy in combination with microfluidics and automated image analysis to quantitatively track the single-cell growth and gene expression dynamics of different target promoters of the LexA SOS response regulator in E. coli under mild DNA damage induced by the antibiotic ciprofloxacin (CIP). We find that, at the single-cell level, LexA target promoters exhibit stochastic bursts in protein production with specific quantitative characteristics. First, the durations of protein production bursts are short, identical for all promoters, and independent of CIP levels. Second, the heights of the production peaks are exponentially distributed for each promoter, and independent of CIP level, but with different average heights for different promoters. Third, the frequency of the production bursts increases with CIP level for all promoters, but differs across promoters. Importantly, we show that these observations are inconsistent with popular equilibrium models of bacterial gene regulation that assume that the dynamics of binding and unbinding of TFs is fast relative to the time-scale of TF concentration fluctuations. Instead, all observations can be quantitatively fit by a relatively simple model in which DNA damage events lead to short transient dips in LexA concentration, and an expression burst occurs in a cell whenever LexA unbinds from the target promoter during such a short dip in LexA concentration. Moreover, because these transient dips in LexA concentration occur on the same time-scale as the stochastic unbinding of LexA from promoters, the response of a target promoter to an individual DNA damage event is stochastic and depends in a complex manner on the strengths of its LexA binding sites and the duration of the event. Consequently, the expression levels of different LexA target genes in a given cell reflect distinct statistics of the frequency and durations of DNA damage events in the recent history of that cell. Our results show that, even in the simple scenario where a single TF is induced, different target promoters can exhibit distinct stochastic responses that depend on the precise kinetics of the induction events.