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Figure 7 | BMC Microbiology

Figure 7

From: Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio

Figure 7

Extent of regulatory conservation for significantly increased or decreased targets. In every panel, the x-axis shows the gene expression ratio for E. coli K-12 Δlrp relative to that in the same strain complemented by E. coli lrp (pEcoLrp). The y-axes indicate the equivalent ratio, where the complementation is by vector alone (pCC1) or the lrp alleles from V. cholerae (pVchLrp) or P. mirabilis (pPmiLrp). Full complementation relative to that by pEcoLrp would yield a slope of 1.0 for the linear fit. A. This column shows responses of the gene set yielding statistically-significant increases in expression associated with lrp mutation in E. coli, as reflected by an expression ratio significantly above 1.0 on the x-axis. This set includes genes that are repressed (directly or indirectly) by E. coli Lrp. B. This column includes the set of genes showing significant decreases in expression associated with lrp mutation in E. coli, indicating direct or indirect activation by E. coli Lrp. C. This column shows the set of 57 genes recognized in RegulonDB [71, 72] as being directly controlled by Lrp, whether the control is positive or negative. This set includes genes that are controlled by Lrp, but not under the growth conditions used by us, so the cluster of genes showing little or no effect of Lrp is not surprising [66, 69]. The relative transcript abundances were estimated from at least three independent biological replicas using a linear model similar to one introduced before [141, 142]. Significantly expressed genes were identified at a fixed false discovery rate of 5% at the 90th percentile [138]. Details of the statistical analysis of these data are in the text, and a list of the 57 RegulonDB Lrp targets is in the Methods section.

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