In E. coli, our group and Kahramanoglou et al. investigated a potential role for Dcm in transcriptional regulation (Kahramanoglou et al., 2012; Militello et al., 2012). In summary, the two reports indicate that the loss of Dcm causes an increase in gene expression of several categories of genes, most notably ribosomal protein genes. These observations were important as they indicate that Dcm can influence
gene expression and that Dcm is normally repressive. In these studies, the effect of Dcm on gene expression was primarily restricted to stationary phase. Kahramanoglou et al. proposed that Dcm represses expression of the stationary phase sigma factor rpoS, and the loss of Dcm-mediated repression results in the up-regulation of rpoS and a downstream change in stationary phase gene expression Selleck PI3K inhibitor (Kahramanoglou et al., 2012). Yet, the relationship between 5-methylcytosine and gene expression is still relatively unexplored, and many questions remain. In particular, we are interested in phenotypes
associated with loss of Dcm. Dcm does not seem to have an effect on growth rate, the ability of cells to enter stationary phase, or the ability of cells to persist in stationary phase [K.T. Militello & R.D. Simon, unpublished data and (Kahramanoglou et al., 2012)]. We previously identified genes that have 5′CCWGG3′ recognition sites in the promoter region, and these targets are potentially regulated by cytosine DNA methylation (Militello et al., TAM Receptor inhibitor 2012). One identified target from this analysis was the sugE gene. The sugE gene has one Dcm site c. 10 nucleotides upstream from the transcription
start site and three in the gene body (Supporting Information, Fig. S1A). The E. coli sugE gene was originally identified as a suppressor of groEL (Greener et al., 1993). SugE is a membrane transporter with almost four predicted membrane spanning regions and is a member of the small multidrug resistance family (Bay et al., 2008). SugE RNA is expressed at stationary phase (Table 2) (Greener et al., 1993) and thus could potentially be regulated by Dcm. The function of the E. coli sugE gene is a bit of a mystery. In an initial study of E. coli drug transporters, SugE-mediated resistance to quaternary ammonium compounds (QACs) and ethidium bromide (ETBR) was not observed when sugE was overexpressed (Nishino & Yamaguchi, 2001). However, Chung and Saier reported that sugE overexpressing cells have increased resistance to several QACs (Chung & Saier, 2002), but not ETBR. Thus, the original model has been that the E. coli SugE protein generates resistance to a narrow range of QACs, but does not generate cells resistant to other compounds such as ETBR. However, not all subsequent data fit with this simple model, especially with respect to a lack of an effect of SugE on ETBR resistance. For example, overexpression of the Citrobacter freundii sugE homolog in E.