Strain construction: The CI-YFP fusion protein (Fig. 1B) was constructed by PCR, and contained the entire coding sequence of the wild-type cI gene fused directly to the coding sequence of the yfp gene (from pDH5 plasmid, University of Washington Yeast Resource Center). The cI-yfp gene was expressed from the tightly regulated P LtetO-1 promoter on the pZS21 plasmid (1), which is stable and difficult to cure. Integration of CFP with the P R promoter was performed as previously described (2). Since the cfp gene is chromosomally integrated, and the repressor concentration is independently measured, the results are not affected by possible variations in plasmid copy number or plasmid loss after the end of induction of cI-yfp expression. Full induction of cI-yfp expression by anhydrotetracycline (aTc) was sufficient to repress CFP production in the λ-cascade strain to undetectable levels. When not induced, the cI-yfp plasmid had no effect on CFP expression. Thus, the strain allows exploration of the full dynamic range of CFP regulation.The O R 2*-λ-cascade strain ( Fig. S3) was constructed by site-directed mutagenesis of the P R promoter (Stratagene QuikChange Kit) with the following primers:This created a mutation which was previously designated as 'VN' (3). The underlined portion of the primers represents O R 2 and the bold nucleotide is the site of the point mutation that changes a G to a T. The 'symmetric branch' strain ( Fig. 4D) was strain MRR containing plasmid pZS21-cIYFP-Y66F. MRR contains CFP and YFP at separate, but equivalent, loci, approximately equidistant from the origin of replication, each under wild-type P R promoters (2). Plasmid pZS21-cIYFP-Y66F was identical to pZS21-cIYFP, except that site-directed mutagenesis was used to introduce a single point mutation converting the tyrosine at YFP position 66 (in the YFP chromophore) to phenyalanine, thereby eliminating repressor fluorescence.Experimental procedure and image acquisition: Cultures were grown overnight in LB + 15 µg/mL kanamycin at 37°C from single colonies, and diluted 1:100 in MSC media (M9 minimal medium + 0.6% succinate + 0.01% casamino acids + 0.15 µg/ml biotin + 1.5 µM thiamine). Cultures were grown to OD 600 ~0.1 at 32°C, and then induced if necessary. Induction consisted of adding aTc to a final concentration of 100 ng/mL for ~3 minutes at ambient temperature, followed by 2 washes with MSC to remove aTc (Fig. 1C). Cells were allowed to grow until just prior to the production of the CI-repressed gene(s), then diluted to give ~1 cell per visual field when placed between a coverslip and 1.5% low melt MSC agarose. Growth of microcolonies was observed by fluorescence microscopy at 32ºC using a Leica DMIRB/E automated fluorescence microscope (Fig. 1D and Fig. S1). Cell-cycle period (doubling time) was 45±10min for all strains. Custom Visual Basic software was written to control the microscope and related equipment (Ludl motorized stage and Hamamatsu Orca II CCD camera), via ImagePro Plus and ScopePro packages (Media Cybernetics). In most cas...

Quantitative single-cell time-lapse microscopy is a powerful method for analyzing gene circuit dynamics and heterogeneous cell behavior. We describe the application of this method to imaging bacteria by using an automated microscopy system. This protocol has been used to analyze sporulation and competence differentiation in Bacillus subtilis, and to quantify gene regulation and its fluctuations in individual Escherichia coli cells. The protocol involves seeding and growing bacteria on small agarose pads and imaging the resulting microcolonies. Images are then reviewed and analyzed using our laboratory's custom MATLAB analysis code, which segments and tracks cells in a frame-to-frame method. This process yields quantitative expression data on cell lineages, which can illustrate dynamic expression profiles and facilitate mathematical models of gene circuits. With fast-growing bacteria, such as E. coli or B. subtilis, image acquisition can be completed in 1 d, with an additional 1–2 d for progressing through the analysis procedure.

Gene regulatory circuits can use dynamic, and even stochastic, strategies to respond to environmental conditions. We examined activation of the general stress response mediated by the alternative sigma factor, σB, in individual Bacillus subtilis cells. We observed that energy stress activates σB in discrete stochastic pulses, with increasing levels of stress leading to higher pulse frequencies. By perturbing and rewiring the endogenous system, we found that this behavior results from three key features of the σB circuit: an ultrasensitive phosphorylation switch; stochasticity (“noise”), which activates that switch; and a mixed (positive and negative) transcriptional feedback, which can both amplify a pulse and switch it off. Together, these results show how prokaryotes encode signals using stochastic pulse frequency modulation through a compact regulatory architecture.