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. 2012 Mar 27;84(3):463–485. doi: 10.1111/j.1365-2958.2012.08036.x

Fig. 2.

Fig. 2

Architecture and DNA sequences of PhoP-activated promoter regions. DNA sequences corresponding to the 23 promoters analysed in this study. To facilitate the comparison of the 23 promoters, we aligned the corresponding sequences with respect to the predicted −10 hexamer using the 5′ most edge of this element as a referential landmark instead of the typically used transcription start site (Gaston et al., 1990; Liu et al., 2004). The transcription start site identified in Fig. S1 is indicated in green. (Transcription start sites for the pipD and rstA promoters are also included, data not shown.) This includes S1 nuclease protection data previously reported for phoP (Soncini et al., 1995; Garcia Vescovi et al., 1996), pmrD (Kato et al., 2003) and orgB (Aguirre et al., 2006) promoters as well as primer extension data reported for mgtA (Lejona et al., 2003), iraP (Tu et al., 2006) and ssrB (Feng et al., 2003; Bijlsma and Groisman, 2005) promoters. The PhoP box corresponding to regions protected by PhoP-P shown in Fig. S3 is indicated in blue. This also includes DNase I footprinting analysis previously reported for phoP (Lejona et al., 2003), ugtL (Shi et al., 2004), pagC (Perez et al., 2008), pmrD (Kato et al., 2003), ssrB (Bijlsma and Groisman, 2005), iraP (Tu et al., 2006) and orgB (Aguirre et al., 2006) promoters [as well as electrophoretic mobility shift assays (EMSA) analysis reported for the mgtA promoter (Lejona et al., 2003), and for the downstream PhoP box in the pagC promoter (this work, data not shown)]. The PhoP box orientation is indicated with blue arrows. The predicted −35 hexamer is underlined in red and the predicted −10 hexamer is indicated in red (Table 2). Activation PhoP boxes sharing common patterns including orientation, phasing and/or location with respect to the RNAP are indicated with grey boxes. The promoters were divided into five classes based on their shared cis-acting features. From top to bottom: Architecture I, Architecture II, Architecture III, Architecture IV and Architecture V.