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“In Escherichia coli, cytosine DNA methylation is catalyzed by the DNA cytosine methyltransferase (Dcm) protein and occurs at the second cytosine in the sequence 5′CCWGG3′. Although the presence of cytosine DNA methylation was reported over 35 years ago, the biological role of 5-methylcytosine in E. coli remains unclear. To gain insight into the role of cytosine DNA methylation in E. coli, we (1) screened the 72 strains of the ECOR collection and 90 recently isolated environmental samples for the presence

of the full-length dcm gene using the polymerase chain reaction; (2) examined the same H 89 order strains for the presence of 5-methylcytosine at 5′CCWGG3′ sites using a restriction enzyme isoschizomer digestion assay; and (3) quantified the levels of 5-methyl-2′-deoxycytidine in selected strains using liquid chromatography tandem mass spectrometry. Dcm-mediated cytosine DNA methylation is conserved in all 162 strains examined, and the level of 5-methylcytosine ranges from 0.86% to 1.30% of the cytosines. We also demonstrate that Dcm reduces the expression of ribosomal protein genes during stationary phase, and this may explain the highly

conserved nature of this DNA modification pathway. DNA bases are modified by postreplicative methylation by enzymes selleck compound termed DNA methyltransferases. In prokaryotes, the most common modified DNA bases are 6-methyladenine and 5-methylcytosine (5mC). The most recognized role of modified DNA bases is in restriction-modification (R-M) systems (Ishikawa et al., 2010). In each R-M system, there Etomidate is a restriction endonuclease that cleaves foreign DNA and a site-specific DNA methyltransferase that prevents cleavage of host DNA, and in some cases controls expression of the R-M system (O’Driscoll et al., 2005). However, some DNA methyltransferases are not found in conjunction with a cognate restriction enzyme and are termed solitary DNA methyltransferases. In addition to DNA adenine methyltransferase

(Dam), Escherichia coli possesses another solitary DNA methyltransferase termed Dcm for DNA cytosine methyltransferase (Marinus & Lobner-Olesen, 2009). The presence of Dcm was discovered in 1973 by Marinus & Morris. The dcm gene of E. coli K-12 contains 1419 base pairs, and the predicted protein is 472 amino acids (Bhagwat et al., 1986; Hanck et al., 1989). The protein contains ten conserved motifs and a catalytic cysteine residue that is found in all cytosine-5 DNA methyltransferases (Posfai et al., 1989). The Dcm protein methylates the internal C in the sequence 5′CCWGG3′ where W = A/T (Palmer & Marinus, 1994). 5mC is occasionally spontaneously deaminated in an existing C:G base pair, and a T:G mismatch is formed. The dcm gene is in an operon with the very short patch repair (vsr) gene and is controlled by the same promoter.