, 2012). In total, the data demonstrate that Dcm influences sugE expression, and the main effect is at stationary phase. This repressive effect of Dcm on gene expression is similar to the repressive effect observed by selleck chemicals our laboratory and Kahramanoglou et al. on ribosomal protein genes at stationary phase and suggests that DNA methylation is normally repressive and has an important role during stationary phase (Kahramanoglou et al., 2012; Militello et al., 2012). The only known
activity of Dcm is methylation of 5′CCWGG3′ sites in DNA. However, some DNA methyltransferases can influence gene expression in a DNA methylation-independent manner. For example, a mutant EcoRII methyltransferase that is not able to methylate DNA can still repress transcription of its own gene (Som & Friedman, 1994). Also, the human DNMT2 enzyme, which has weak DNA methyltransferase activity (Hermann et al., 2003), is able to methylate tRNAAsp and a limited set of other tRNAs (Schaefer et al., 2010). To find more directly test the model that Dcm-mediated DNA methylation represses sugE expression, wild-type cells were grown in the absence and presence of the DNA methylation inhibitor 5-azacytidine to both early logarithmic phase and early stationary phase, and sugE RNA levels were quantified by qPCR (Table 2B). We
observed c. 3–4 × more sugE RNA in the 5-azacytidine treated cells at both early logarithmic and early stationary phase (P < 0.05). Although it was not surprising to observe up-regulation of sugE in the presence of 5-azacytidine Beta adrenergic receptor kinase at stationary phase based on the qPCR data given above, we were surprised to see an effect at early logarithmic phase, and the magnitude of the effect was similar to that at early stationary phase. This may be due to
the fact that there is indeed a small repressive effect of DNA methylation on sugE expression at early logarithmic phase, and/or stationary phase cells that are not rapidly dividing are not as likely to incorporate as much 5-azacytidine into DNA. In addition, 5-azacytidine is known to be toxic to E. coli in killing assays (Bhagwat & Roberts, 1987; Betham et al., 2010). In our experiments, there are lower A600 nm readings only after c. 2.5 h of growth (Fig. S2), which is after the point in which the early logarithmic phase RNA was isolated. As a whole, the 5-azacytidine data are consistent with the dcm knockout data which suggest Dcm-mediated DNA methylation represses sugE expression. Yet, we cannot rule out that sugE expression is also increased by cell stress, changes in growth rate, and/or Dcm has both DNA methylation dependent and independent functions. Next, we were interested in determining how Dcm influences sugE expression. Although we were originally intrigued by the presence of 5′CCWGG3′ sites in the sugE promoter and gene body, Kahramanoglou et al.