The restriction–modification genes of Escherichia coli K-12 may not be selfish: They do not resist loss and are readily replaced by alleles conferring different specificities

Abstract

Type II restriction and modification (R-M) genes have been described as selfish because they have been shown to impose selection for the maintenance of the plasmid that encodes them. In our experiments, the type I R-M system EcoKI does not behave in the same way. The genes specifying EcoKI are, however, normally residents of the chromosome and therefore our analyses were extended to monitor the deletion of chromosomal genes rather than loss of plasmid vector. If EcoKI were to behave in the same way as the plasmid-encoded type II R-M systems, the loss of the relevant chromosomal genes by mutation or recombination should lead to cell death because the cell would become deficient in modification enzyme and the bacterial chromosome would be vulnerable to the restriction endonuclease. Our data contradict this prediction; they reveal that functional type I R-M genes in the chromosome are readily replaced by mutant alleles and by alleles encoding a type I R-M system of different specificity. The acquisition of allelic genes conferring a new sequence specificity, but not the loss of the resident genes, is dependent on the product of an unlinked gene, one predicted

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

“…Host cell killing was also shown with the type IV enzyme McrBC by the introduction of a DNA methylation gene (96). Although such selfish behavior appears to be a widespread phenomenon with type II R-M systems, it is not common in type I or III enzymes (97). In the latter systems, the MTase and the REase are subunits of the same protein complex, and the intracellular ratios of MTase to REase do not change over time upon the loss of the R-M locus, a prerequisite for function as an addiction module.…”

“…In the latter systems, the MTase and the REase are subunits of the same protein complex, and the intracellular ratios of MTase to REase do not change over time upon the loss of the R-M locus, a prerequisite for function as an addiction module. Studies of EcoKI, one of the earliest-characterized type I enzymes, revealed that the enzyme does not behave as a selfish element (97). Similarly, EcoR124I, another well-studied type IC enzyme encoded on a large plasmid, does not seem to exhibit postsegregational killing (98).…”

“…The widespread occurrence of R-M systems among eubacteria, archaea, and certain viruses of unicellular algae (46,97,187,188) may hint at their other functions in addition to cellular defense. These additional roles could be better understood by looking into the evolutionary route by which a particular R-M system acquired a new biological function.…”

Immigration control of DNA in bacteria: self versus non-self

“…It has been shown that the bacterial chromosome becomes susceptible to restriction as cell growth dilutes the modification enzyme (Handa et al, 2000). However, while the loss of genes that specify some simple R-M systems leads to cell death, the loss of genes that specify other, more complex, R-M systems causes no detectable viability problem (O'Neill et al, 1997 ;Kulik & Bickle, 1996 ;Makovets et al, 1998). In this by EcoKI and thus forms plaques with reduced efficiency (e.o.p.…”

Maintenance Forced by a Restriction-Modification System Can Be Modulated by a Region in Its Modification Enzyme Not Essential for Methyltransferase Activity

“…However, the level of such killing varies among RM systems, presumably reflecting the complexity of the parasite-host interaction (and we will analyze one example in the present work). Postsegregational killing has not been proven for type I RM systems examined so far (34,53). Host attack by EcoKI, one of these type I restriction enzymes tested, is prevented by its proteolytic cleavage (11).…”