, 1990). The Vsr protein is an endonuclease that is necessary to remove the new thymine residue (Hennecke et al., 1991) and thus compensates for the mutagenic potential of 5mC. There is evidence that Dcm itself is required for robust very short patch repair of mismatched bacteriophage heteroplexes (Jones et al., 1987; Lieb, 1987; Zell & Fritz, 1987), but this relationship has not been observed in all reports (Sohail Ku-0059436 mw et al., 1990). Nonetheless, the sequence

5′CCWGG3′ is still a mutational hot-spot sequence, because not all mismatches are repaired (Lieb & Bhagwat, 1996). The biological role of the dcm gene and 5′CCWGG3′ cytosine DNA methylation in E. coli remains unclear. The dcm gene is not essential as mutant, deletion, and knockout strains are viable (Marinus & Morris, 1973; Baba et al., 2008). Interestingly, the dcm gene and cytosine

DNA methylation are absent from E. coli B (Doskocil & Sormova, 1965; Fujimoto et al., 1965), a host strain used extensively to study bacteriophages T1–T7 (Daegelen et al., 2009). Genome sequencing of E. coli B (REL606) shows that when compared to E. coli strain K-12 MG1665, it has an IS1-associated 41-kbp deletion from uvrY to hchA that comprises ~0.9% of the genome including the dcm gene and 21 flagellar genes Gefitinib research buy (Studier et al., 2009). The loss of the dcm operon in E. coli B may have been coupled to the loss of the nearby flagellar and chemotaxis genes, as strains that lack flagellar and chemotaxis genes have an advantage during laboratory evolution experiments (Asakura et al., 2011). Nonetheless, several Phosphatidylinositol diacylglycerol-lyase pieces of evidence suggest that Dcm has a role in modulating the activity of the EcoRII R-M system in K-12 strains, which also targets 5′CCWGG3′ sequences. Experiments by Takahashi et al. (2002) indicate that loss of a plasmid containing

the EcoRII methyltransferase and restriction enzyme genes is higher in dcm+ cells compared to dcm mutant cells, indicating that Dcm protects the genome against attack by this R-M system. Furthermore, Dcm protects the cell from postsegregational killing due to loss of the EcoRII R-M system (Ohno et al., 2008). Also, dcm partially protects DNA from cleavage during entry into a new host containing the EcoRII restriction enzyme (Hattman et al., 1973). However, it is unclear whether there are roles for Dcm beyond the role in the EcoRII R-M system. Therefore, we determined whether the dcm gene and 5mC were present in E. coli clinical strains and strains isolated from water and animal feces (environmental strains). We also tested the hypothesis that dcm influences the process of transcription, as cytosine-5 DNA methyltransferases often have this property. The E. coli Reference Collection (ECOR), a set of E. coli strains isolated from a variety of hosts and geographical locations (Ochman & Selander, 1984), was obtained from the ‘Shiga-toxin producing E. coli’ Center (STEC) at Michigan State University. Environmental strains of E.