The mrr gene of Escherichia coli K-12 is involved in the acceptance of foreign DNA which is modified. The introduction of plasmids carrying the HincII, HpaI, and TaqI R and M genes is severely restricted in E. coli strains that are Mrr+. A 2-kb EcoRI fragment from the plasmid pBg3 (B. Sain and N. E. Murray, Mol. Gen. Genet. 180:35-46, 1980) DNA (39,41,44,45). These two systems were initially called rglA and rglB because they restricted glucoseless, 5-hydroxylmethyl cytosine-containing DNA, present in many T-even phage (42). One system (rglB) was found to produce an endonuclease activity (16). These restriction systems differ from the classically recognized ones since they require modified DNA as the substrate for their action rather than using modification for selfprotection.An additional methylation-specific restriction system of E. coli, Mrr, was described by Heitman and Model (20) and was shown to interfere with the maintenance of certain N6-adenine methylases. The HhaII and PstI N6-adenine methylase genes, when maintained in several E. coli K-12 strains, produced DNA damage as evidenced by induction of the SOS DNA repair response (20). They also demonstrated that several cytosine methylases induced the SOS response. Transposon insertion mapping and Southern blotting were used to position mrr on the E. coli chromosome at 98.5 min.

The BamHI restriction modification system was previously cloned into E. coli and maintained with an extra copy of the methylase gene on a high copy vector (Brooks et al., (1989) Nucl. Acids Res. 17, 979-997). The nucleotide sequence of a 3014 bp region containing the endonuclease (R) and methylase (M) genes has now been determined. The sequence predicts a methylase protein of 423 amino acids, Mr 49,527, and an endonuclease protein of 213 amino acids, Mr 24,570. Between the two genes is a small open reading frame capable of encoding a 102 amino acid protein, Mr 13,351. The M. BamHI enzyme has been purified from a high expression clone, its amino terminal sequence determined, and the nature of its substrate modification studied. The BamHI methylase modifies the internal C within its recognition sequence at the N4 position. Comparisons of the deduced amino acid sequence of M. BamHI have been made with those available for other DNA methylases: among them, several contain five distinct regions, 12 to 22 amino acids in length, of pronounced sequence similarity. Finally, stability and expression of the BamHI system in both E. coli and B. subtilis have been studied. The results suggest R and M expression are carefully regulated in a 'natural' host like B. subtilis.

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