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Fig. 5 | BMC Genomics

Fig. 5

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. 5

Promoter activities of TSS upstream regions. Beta-galactosidase activities of B. japonicum USDA 110 cells harboring plasmids with transcriptional lacZYA reporter fusions measured in exponentially growing cultures. Fifteen TSSs with scores between 0.06 and 0.88 (ordered according to increasing score from top to bottom) were tested. The number of each tested TSS (No.), its Bja_TSS_locus tag, peak height (Peak) and score in Free and Nod as well as the presence of a mapped promoter in its upstream region are indicated. NA, not applicable (indicates that the TSS was not scored under the respective condition; see Additional file 3: Table S3); no, promoter was not mapped upstream of the respective TSS; *, promoter was verified by mutagenesis (see Fig. 4d and Fig. 8); **, the TSS was validated in Free although it was scored only in Nod. The dashed blue vertical line separates the extremely low beta-galactosidase activity values indicating no promoter activity (and thus failed validation of five TSSs) from the higher beta-galactodsidase activity values validating ten TSSs. The dashed red horizontal line separates TSSs with scores below 0.4 belonging to the class of low confidence from the high-confidence TSSs with scores above the cut-off (see also Figs. 6 and 7 below). BjrC68 and BjrC174, previously analyzed sRNAs [16]. For Pcyp, Pint, Pas, 3′-seR and 3′-asR, see Fig. 9 below

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