FIGURE 1.

Predicted secondary structure of the htrA RNA thermometer from Salmonella enterica. (A) The 5′ UTR of the htrA mRNA is shown from the standard transcriptional start site to one codon past the AUG start codon. The fourU element and the Shine–Dalgarno (SD) sequence are labeled. As defined in the text, the lower stem and upper stem nucleotides are labeled, and hairpin loop nucleotides are circled. The single-nucleotide bulge on the 5′ side of the stem is indicated with an arrow. The structure was predicted using mfold 3.0 (Zuker 2003), as shown in Klinkert et al. (2012). (B) The putative structure of the htrA thermometer embedded in the SHAPE structure cassette (Wilkinson et al. 2006; Vachon and Conn 2012). The primer-binding site is shown in blue, and the remainder of the cassette regions are shown in gray. Numbering is from the 5′ end of the SHAPE cassette; this numbering is used throughout the manuscript. The structure shown was predicted using RNAstructure (Reuter and Mathews 2010) at 37°C.