Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis

We used 2D protein gel electrophoresis and DNA microarray technologies to s ystematically analyze genes under glucose repression in Bacillus subtilis. In particular, we focused on genes expressed after the shift from glycolyti c to gluconeogenic at the middle logarithmic phase of growth in a nutrient sporulation medium, which remained repressed by the addition of glucose. We also examined whether or not glucose repression of these genes was mediate d by CcpA, the catabolite control protein of this bacterium. The wild-type and ccpA1 cells were grown with and without glucose, and their proteomes an d transcriptomes were compared. 2D gel electrophoresis allowed us to identi fy 11 proteins, the synthesis of which was under glucose repression. Of the se proteins, the synthesis of four (IolA, I, S and PckA) was under CcpA-ind ependent control. Microarray analysis enabled us to detect 66 glucose-repre ssive genes, 22 of which (glmS, acoA, C, yisS, speD, gapB, pckA, yvdR, yxeF , iolA, B, C, D, E, F, G, H, I, J, R, S and yxbF) were at least partially u nder CcpA-independent control. Furthermore, we found that CcpA and IolR, a repressor of the iol divergon, were involved in the glucose repression of t he synthesis of inositol dehydrogenase encoded by iolG included in the abov e list. The CcpA-independent glucose repression of the iol genes appeared t o be explained by inducer exclusion.