Figure 6. Diversity in Sigma Factor Competition and Correlation.

(A) To systematically analyze competition between sigma factors, we constructed a deletion matrix. Each strain in the matrix is genetically deleted for one sigma factor (rows), and contains a chromosomally integrated fluorescent reporter for another sigma factor (columns). Cells were grown in minimal media with 40 μg/mL MPA. Mean reporter expression was measured by fluorescence microscopy. Each element in the matrix shows the fold change in sigma factor activity upon deletion of another sigma factor relative to wild-type. For instance, the ΔsigB, P_W-yfp strain (row 1, column 3) exhibited ~1.4-fold more fluorescent signal relative to the P_W-yfp reporter strain without deletion. The elements along the “diagonal” of the deletion matrix reflect negative controls on the sigma factors reporter strains’ specificity. Asymmetric interactions are evident from the increased fold change along the ΔsigD row and the σ^W column.

(B) Simulated cross-correlations for asymmetric parameters inspired by the results in (A); see (D), and parameter set B in STAR Methods. A mixture of positive and negative cross-correlations can arise from asymmetric competition for core RNAP. Each trace is the average of 81 cross-correlation functions, calculated from 28,000 simulated cell cycles.

(C) Histogram showing the distribution of the number of sigma factors simultaneously active during pulses in the dynamics displayed in Figure S8C (parameter set B in STAR Methods). Pulse detection threshold was as in Figure 3E, except for σ³, which used a threshold of 0.1 μM.

(D) The asymmetric sigma factor model recapitulates the broad features of the experimental deletion matrix. The deletion matrix was simulated in the model (parameter set B in STAR Methods) by removing each alternative sigma factor one at a time, and then simulating the rest of the sigma factors. Each simulation was run for 28,000 cell cycles. Deletion of σ⁵ increases the activity of all other sigma factors. σ³ is most sensitive to deletion of any other sigma factor. See also Figure S8.