Fig. 6. D9A mutation bypasses an AAN motif in rpoS mRNA.

(a) Schematic representation of rpoS secondary structure and position of Hfq binding sites. (b) Fraction ³²P-labeled rpoS 301RNA bound to DsrA with or without Hfq after 30 s. Mutations in rpoS deleted the upstream AAN motif (Δ(AAN)4), the downstream U₅ loop (ΔU5), or both of these plus an A₆ sequence (ΔΔΔ). (c) E. coli cells (Table S1) containing a chromosomal copy of WT or mutant rpoS::lacZ fusion, with hfq⁺ or hfqD9A alleles in the chromosome for each, were grown overnight at 37 °C on MacConkey agar supplemented with 0.0001% arabinose. Strains used, listed clockwise from WT in Figure, were SG30214, SG30236 SG30233, SG30242, SG30277, SG30279, DJS3056, and DJS3059, all described in Table S1. Red colonies indicate up-regulation of lacZ expression by Hfq and chromosomally derived sRNAs (DsrA, ArcZ and RprA). See Fig. S4 and S5 for further data.