Figure 1. Multiple Alternative Sigma Factors Pulse under Energy Stress.

(A) Alternative sigma factors bind core RNAP to activate target genes, including endogenous targets (left target) and the engineered fluorescent reporters used here (right target).

(B) Multiple distinct alternative sigma factor species (colored shapes) share core RNAP (gray). The “housekeeping” sigma factor σ^A (white) also utilizes core RNAP.

(C) In principle, sigma factor species could share core RNAP by partitioning, with each sigma factor species utilizing some constant fraction of total RNAP (molecular sharing, top). Alternatively, they could share RNAP in time, with one or more sigma factors occupying a large fraction of RNAP for some period, followed by a different sigma factor or factors for another period of time, and so on (time sharing, bottom). Only three distinct species are shown here for simplicity.

(D) Fluorescent reporter expression in growing microcolonies shows heterogeneous activation of seven alternative sigma factors, as indicated, and homogeneous activation of σ^A (bottom right) under energy stress conditions.

(E) Time-lapse analysis reveals stochastic pulsing of alternative sigma factors in individual cell lineages. Here, each plot shows sigma factor activity time traces derived from analysis of corresponding fluorescent reporter genes in three different cell lineages (different line shades). For each plot, the y axis shows rate of fluorescent protein production, approximating instantaneous sigma factor activity. Note that the housekeeping sigma factor σ^A shows much less variability over time. See also Figures S1 and S2.