The role of dam methylation in controlling gene expression

Abstract

The E. coii gene dam encodes an adenine-specific methylase which converts all adenine residues in the sequence GATC into 6-methyl adenine, dam type methylases seem to be ubiquitous in Enterobacteriaceae and Haemophilus, since DNA from these strains cross hybridizes with the cloned dam gene and they contain DNA resistant to MboI cleavage, which only cleaves non-methylated DNA [1]. However, dam methylation is absent from most species of eubacteria not phylogenetically related to E. coli and presumably evolved late in prokaryotic evolution [2]. At least, one reason why people have become more aware of dam (and dcm) methylation in the last decade is because certain restriction enzymes are sensitive to DNA methylation and hence overlapping dam and restriction sites are not cleaved [3]. The primary phenotype of dam mutations is a nearly total loss of adenine methylation [4]. However, a small residual amount of adenine methylation appears to remain in dam strains even in strains carrying an insertion of Tn9 in the dam gene [5]. There are numerous secondary phenotypes associated with dam mutations and they are presumably due to the lack of adenine methylation. These secondary phenotypes include increased sensitivity to UV and 2-amino purine, increasedspontaneous mutability, decreased stability of plasmids, especially those of the Rl family, increased spontaneous induction of 2 and increased recombination frequency [4, 6]. The presence of a plasmid carrying the wild type dam gene reverses these secondary phenotypes [7]. Second site mutations which suppress some of these secondary phenotypes (but not the primary defect, i.e., the lack of adenine methylation) have been isolated in the genes mutL, m a t h and routs [6]. The dam gene is not essential, as shown by the isolation of a Tn9 insertion in the gene [8], but dam mutations are not viable in combination with recA, lexA, recB, C or poiA mutations. These double mutants become viable, however, in the presence of mutL or routs alleles [9]. The inviability of double dam, rec mutations became more comprehensible with the observation that dam mutations result in enhanced expression of genes of the SOS regulon (i.e., recA, lexA, uvrA, uvrB, uvrD, sulA, dinA and dinF) [10], implying that a dam mutation results in a requirement for higher levels of these proteins. More recently, a third phenotype for the dam mutations has been described in the literature: that of controlling the level of expression of a miscellaneous selection of genes with GATC sequences in their promoter regions. It is this third phenotype which is the subject of this paper, but initially it is worth summarizing the evidence for the dam methylation affecting other phenot~,~,~ of the E. coli bacteria.