Specificity: EcoKI restriction, encoded by the hsdRMS genes, attacks DNA that is not protected by adenine methylation at the appropriate recognition site (AAC[N6]GTGC or GCAC[N6]GTT) (1). McrA, McrBC, and Mrr, encoded by mcrA, mcrBC, and mrr (2-6), are methylation-requiring systems that attack DNA only when it is methylated at specific positions. All three of the latter systems restrict DNA modified by CpG methyltransferase (M.Sss I) to contain methylcytosine in CpG dinucleotides (5). Mrr will also attack DNA with methyladenine in specific sequences (4,6). One or more of these is present in most commonly used strains of E. coli. (7-12).

The methylation-requiring restriction systems are sequence specific; McrA, McrBC, and Mrr do not restrict DNA modified at dcm sites, nor does Mrr restrict DNA modified at dam, EcoKI, or EcoRI sites. In addition to restricting M.Sss I-modified DNA, McrA restricts DNA modified by the HpaII methylase (5´ C^meCGG; 2), while McrBC restricts DNA modified at the sequence 5´ R^meC (2,3,13). McrA and McrBC apparently do not distinguish between 5-methylcytosine and 5-hydroxymethylcytosine; McrBC also restricts DNA containing N4-methylcytosine in appropriate sequences (3). Mrr restricts DNA modified by a variety of adenine methyltransferase and several 5-methylcytosine methyltransferase but no consensus recognition sequence has yet been deduced (4,6).

Almost all laboratory strains of E. coli are derivatives of wild isolates K-12 or B. They do not carry EcoRI or other type II restriction systems, which were identified in other wild isolates.

When to worry: The mcr and mrr loci have been shown to reduce recovery of methylated sequences from mammals (8,9,11,14) and plants (9,15) in cloning experiments. In general, it is wise to use a strain lacking the Mcr and Mrr systems when cloning genomic DNA from an organism with methylcytosine: this includes all mammals and higher plants, and many prokaryotes (16) but not the important experimental organisms Drosophila melanogaster (17) and Saccharomyces cerevisiae (18). In addition, such a strain should be used when using cytosine methylases to generate novel specificities (19) or to protect cDNA from subsequent digestion (20). Since methyladenine is present in many bacteria and lower eukaryotes, Mrr-mediated restriction should also be considered when cloning genomic DNA from these organisms.

When not to worry: Note that the foreign methylation pattern will be lost (and the E. coli methylation pattern acquired) upon replication of the clone in E. coli, unless the clone carries methyltransferase activity. Once successfully introduced, clones can be moved freely among Mcr⁺ Mrr⁺ E. coli strains, since the methylation pattern will no longer be foreign. Be sure the DNA is K-modified before trying to introduce it into a K-restricting strain.

Properties of strains: The table here summarize known McrA, McrBC, and EcoKI strain phenotypes. Mrr phenotype is indicated under "background" when it is known. Only a few strains have been explicitly tested, but it is reasonable to assume that most strains are Mrr⁺. We have not tested for the prophage-encoded EcoP1 endonuclease; to our knowledge, only JM103 (not in the table) carries this. Strains with a deletion (D) of the mcrBC-hsdRMS-mrr cluster were shown to be more permissive hosts than strains with point mutations in hsd and mcrB (9,11,14).

References
1. Bickle, T. (1993) in Nucleases eds Linn, S.M., Lloyd, R.S. and Roberts, R.J. (CSH, NY) p. 89-109.
2. Raleigh, E.A. and Wilson, G. (1986) Proc. Natl. Acad. Sci. USA 83, 9070-9074.
3. Raleigh, E.A. (1992) Mol. Microbiol. 6, 1079-1086.
4. Heitman, J. and Model, P. (1987) J. Bacteriol. 169, 3243-3250.
5. Kelleher, J. and Raleigh, E.A. (1991) J. Bacteriol. 173, 5220-5223.
6. Waite-Rees, P. et al. (1991) J. Bacteriol. 173, 5207-5219.
7. Raleigh, E.A. et al. (1988) Nucl. Acids Res., 16, 1563-1575.
8. Whittaker, P.A. et al. (1988) Nucl. Acids Res., 16, 6725-6736.
9. Woodcock, D.M. et al. (1989) Nucl. Acids Res., 17, 3469-3478.
10. Raleigh, E.A., Trimarchi, R., and Revel, H. (1989) Genetics 122, 279-296.
11. Grant, G.N. et al (1990) Proc. Natl. Acad. Sci. USA 87, 4645-4649.
12. Krüger, T. et al. (1992) Gene 114, 1-12.
13. Sutherland, E. et al. (1992) J. Mol. Biol. 225, 327-348.
14. Doherty, J.P. et al. (1992) Gene 98, 77-82.
15. Graham, M.W. et al. (1989) Plant Mol. Biol. Reporter 8, 18-27.
16. Ehrlich, M. and Wang, R.Y. (1981) Science 212, 1359-1357.
17. Urieli-Shoval, Y. et al. (1982) FEBS Lett. 146, 148-152.
18. Proffitt, J.H. et al. (1984) Mol. Cell. Biol. 4, 985-988.
19. McClelland, M., Nelson, M. and Raschke, E. (1994) Nucl. Acids Res. 22, 3640-3659.
20. Meissner, P.S. et al. (1987) Proc. Natl. Acad. Sci. USA 84, 4171-4175.
21. J. Alber, personal communication.