Catabolite repression and activation in Bacillus subtilis: dependency on CcpA, HPr, and HprK

Abstract

Previous studies have suggested that the transcription factor CcpA, as well as the coeffectors HPr and Crh, both phosphorylated by the HprK kinase/phosphorylase, are primary mediators of catabolite repression and catabolite activation in Bacillus subtilis. We here report whole transcriptome analyses that characterize glucose-dependent gene expression in wild-type cells and in isogenic mutants lacking CcpA, HprK, or the HprK phosphorylatable serine in HPr. Binding site identification revealed which genes are likely to be primarily or secondarily regulated by CcpA. Most genes subject to CcpA-dependent regulation are regulated fully by HprK and partially by serine-phosphorylated HPr [HPr(Ser-P)]. A positive linear correlation was noted between the dependencies of catabolite-repressible gene expression on CcpA and HprK, but no such relationship was observed for catabolite-activated genes, suggesting that large numbers of the latter genes are not regulated by the CcpA-HPr(Ser-P) complex. Many genes that mediate nitrogen or phosphorus metabolism as well as those that function in stress responses proved to be subject to CcpA-dependent glucose control. While nitrogen-metabolic genes may be subject to either glucose repression or activation, depending on the gene, almost all glucose-responsive phosphorus-metabolic genes exhibit activation while almost all glucose-responsive stress genes show repression. These responses are discussed from physiological standpoints. These studies expand our appreciation of CcpA-mediated catabolite control and provide insight into potential interregulon control mechanisms in gram-positive bacteria.

FIG. 1.

Proposed sensory transduction pathway by which exogenous glucose is believed to activate the CcpA transcription factor to promote catabolite repression (CR) or catabolite activation (CA) by binding to a catabolite responsive element (CRE) in the control region of a target gene. Proteins primarily involved are (i) the glucose phosphotransferase system, including enzyme I, HPr, and IIBCA^Glc, (ii) glycolytic enzymes, (iii) the ATP-dependent fructose 1,6-bisphosphate-dependent HPr/Crh kinase/phosphatase HprK, and the two small PTS protein targets of HprK that independently bind to CcpA to activate it for binding to CREs, HPr and Crh (see references , , , , , , , and for reviews).

FIG. 2.

Correlation between CcpA- and HprK dependencies for the glucose effects on gene expression using regression analysis. All genes showing greater than 2-fold glucose effects with large signals (83) were used for the analysis. A: Catabolite-repressed genes; B: catabolite-activated genes. Derived averaged values obtained from the microarray experiments were plotted as indicated on the x and y axes. Best-fit lines (dashed lines) as well as best-fit lines that pass through the origin (solid lines) are shown. The R² values for each line are presented. Larger R² values (maximal value of 1.0) indicate greater conformity of the lines to the data.

FIG. 3.

Correlation between CcpA and HprK dependencies for nitrogen-metabolic genes subject to CR. The format of presentation is as in Fig. 2.