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Fig. 4 | BMC Genomics

Fig. 4

From: Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation

Fig. 4

Promoter motifs predicted de novo based on genomic regions upstream of mapped TSSs. a Schematic representation of a bacterial promoter: upstream 6-mer box (distance to TSS denoted with dashed arrow), downstream 6-mer box (distance to TSS denoted with solid arrow). b Promoter location distribution. Location is a combination of positions of an upstream box (length of dashed arrow in panel a and a downstream box (length of solid arrow in panel a. Position is shown relative to TSS, in 5′ to 3′ direction. Locations are shown for TSS upstream regions of all TSSs (“all classes”, black circles), and TSSs active in nodules only (“Nod only”, grey circles). Circle size is proportional to number of motifs mapping in specific positions (location). c Four motifs (I to IV) similar to typical RpoD-dependent promoters were found when the regions upstream of all TSSs were analyzed. d A predicted RpoD-dependent promoter (Pas) with an extended downstream (–10) box (motif III in panel a was verified experimentally. The sequence upstream of the mapped TSS Bja_TSS_3939 (marked with a bent arrow) is shown. The –35 and –10 box of the predicted Pas are in bold and italics, and the GC extension of the –10 box is underlined. The 63 nt region upstream of the TSS was transcriptionally fused to the lac operon and beta-galactosidase activity measurements in B. japonicum were performed. The introduced mutations in the GC extension are indicated. Shown are results from three independent experiments with technical duplicates with error bars depicting the standard deviation. e A motif detected upstream of leaderless mRNAs. f A motif similar to RpoN-dependent promoters was found, when the regions upstream of TSSs detected in Nod only were analyzed

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