Figure 1.

Rho-dependent terminator in the pgaA leader region. (A) Graph showing the distributions of cytosine and guanine residues (in 78-nt windows) (Alifano et al. 1991) in the upstream section of the pgaABCD operon. (B) Sequence of the pgaA leader region. Pyrimidine (YC) dimers (highlighted in yellow) that are “in phase” and could constitute rut subsites are linked by blue or red lines. The predicted termination site is ∼150 nt downstream from the position identified by Peters et al. (2012), a difference likely ascribable to 3′ end trimming of Rho-terminated transcripts by exonucleases in vivo (discussed by Peters et al. 2012). The positions of CsrA-binding sites (core portion highlighted in green) are from Wang et al. (2005). (C) Hairpin-like RNA motif predicted by Mfold in the upstream section of the pgaA leader rut site (see also Supplemental Fig. S2).