Fig. 6

CsrA regulates iron metabolism. a Summary of the effects of CsrA and Fur on iron-related genes. Squares near gene names show effect of CsrA on translation (RPF, left), RNA abundance (RNA, top), RNA stability (stability, bottom), and/or translation efficiency (TE, right). Octagons indicate the effects of Fur-Fe²⁺ on RNA abundance adapted from Seo et al.⁴⁹ Purple indicates repression and green indicates activation by CsrA or Fur. Asterisks indicate that CsrA CLIP-seq peak(s) are associated with the gene. b qRT-PCR analysis of steady-state ftnA, ftnB, dps, and bfr RNA levels normalized to 16s rRNA. Error bars show standard deviation from the mean of three independent experiments. Two tailed Student’s t test was used to determine statistical significance: ftnA (n = 3, p = 0.0024), ftnB (n = 3, p = 0.005), dps (n = 3, p = 0.004), and bfr (n = 3, p = 0.0016). c, e qRT-PCR analysis of ftnB (c) and dps (e) RNA stability in wild-type (WT) and csrA mutant strains. Error bars show standard deviation from the mean of two independent experiments. Half-life was manually determined from the linear component of the decay curve. Two tailed Student’s t test was used to determine statistical significance of the change in half-life: ftnB (n = 2, p = 0.0011), and dps (n = 2, p = 0.0258). d Western blot showing 3xFLAG-FtnB levels throughout the growth curve (EL early log, ML mid-log, T transition to stationary phase, and S stationary phase) in WT and csrA mutant strains. Full blots are shown in Supplementary Fig. 18. Densitometry was normalized to RpoB levels before calculating fold changes. This experiment was repeated twice with similar results