The Escherichia coli chromosome contains specific, unmethylated dam and dcm sites

Improved electro-transformation of highly DNA-restrictive corynebacteria with DNA extracted from starved Escherichia coli

Differences of up to 33 000-fold in electro-transformability of highly DNA restrictive corynebacteria are observed in the DNA of a shuttle plasmid extracted from Escherichia coli hosts propagated in different nutritional conditions. Growth of the host in minimal medium increases plasmid transformability, whereas growth on rich media decreases it. In the E. coli DH5 alpha host, the starvation-dependent increase DNA transformability is reverted by supplementing with methionine, an obligate 5-adenosyl-methionine (SAM) precursor. This suggests that an E. coli nutritionally modulated SAM-dependent DNA-methyltransferase may be involved in this phenomenon.

Both an altered DNA structure and cellular proteins are involved in protecting a triplex forming an oligopurine-rich sequence from Dam methylation in E. coli

When the 4-bp Dam recognition sequence was placed between two d(GA)7 tracts, it became severely undermethylated in JM101 Escherichia coli cells compared to other Dam sequences in the same plasmid DNA. This site specific undermethylation was also detected on supercoiled molecules in vitro. Mutational analysis indicated that undermethylation is related to the capacity of the oligopurine tract to adopt the H-DNA conformation. In addition, chemical probing of the cells was consistent with a cellular protein bound to the DNA. Therefore it is likely that the combination of altered DNA conformation and a cellular protein leads to Dam-site protection. We also found that the site-specific undermethylation is detectable in certain E. coli strains only.

Overproduction of DNA cytosine methyltransferases causes methylation and C --> T mutations at non-canonical sites

Multicopy clones of Escherichia coli cytosine methyltransferases Dcm and EcoRII methylase (M. EcoRII) cause an approximately 50-fold increase in C --> T mutations at their canonical site of methylation, 5'-CmeCAGG (meC is 5-methylcytosine). These plasmids also cause transition mutations at the second cytosine in the sequences CCGGG at approximately 10-fold lower frequency. Similarly, M. HpaII was found to cause a significant increase in C --> T mutations at a CCAG site, in addition to causing mutations at its canonical site of methylation, CCGG. Using a plasmid that substantially overproduces M. EcoRII, in vivo methylation at CCSGG (S is C or G) and other non-canonical sites could be detected using a gel electrophoretic assay. There is a direct correlation between the level of M. EcoRII activity in cells, the extent of methylation at non-canonical sites and frequency of mutations at these same sites. Overproduction of M. EcoRII in cells also causes degradation of DNA and induction of the SOS response. In vitro, M. EcoRII methylates an oligonucleotide duplex containing a CCGGG site at a slow rate, suggesting that overproduction of the enzyme is essential for significant amounts of such methylation to occur. Together these results show that cytosine methyltransferases occasionally methylate cellular DNA at non-canonical sites and suggest that in E. coli, methylation-specific restriction systems and sequence specificity of the DNA mismatch correction systems may have evolved to accommodate this fact. These results also suggest that mutational effects of cytosine methyltransferases may be much broader than previously imagined.

A cell cycle-regulated bacterial DNA methyltransferase is essential for viability

The CcrM adenine DNA methyltransferase, which specifically modifies GANTC sequences, is necessary for viability in Caulobacter crescentus. To our knowledge, this is the first example of an essential prokaryotic DNA methyltransferase that is not part of a DNA restriction/modification system. Homologs of CcrM are widespread in the alpha subdivision of the Proteobacteria, suggesting that methylation at GANTC sites may have important functions in other members of this diverse group as well. Temporal control of DNA methylation state has an important role in Caulobacter development, and we show that this organism utilizes an unusual mechanism for control of remethylation of newly replicated DNA. CcrM is synthesized de novo late in the cell cycle, coincident with full methylation of the chromosome, and is then subjected to proteolysis prior to cell division.

Regulation of EcoRII methyltransferase: effect of mutations on gene expression and in vitro binding to the promoter region

EcoRII Methyltransferase (M.EcoRII) which methylates the second C in the sequence CCWGG (W = A/T) is autogenously regulated by binding to the 5' regulatory region of its gene. DNase I footprinting experiments demonstrated that purified M.EcoRII protected a 47-49 bp region of DNA immediately upstream of the ecoRIIM coding region. We have studied this interaction with mutants of the enzyme, in vitro by DNA binding and in vivo by investigating the repression in trans of expression of beta-galactosidase from an ecoRIIM-lacZ operon fusion. Two catalytically active mutants failed to repress expression of the fusion whereas catalytically inactive mutants had repressor activity. However, with one of the catalytically inactive mutants, C186S, in which the catalytic Cys was replaced with Ser, and which bound unmethylated CCWGG sequences, repression could only be demonstrated when those sequences in cellular DNA were methylated by supplying a cloned dcm gene in trans. In vitro binding of the DNA fragment containing the ecoRIIM regulatory region was detected only with the mutants that showed repressor activity, including C186S. Results indicate that down-regulation of the gene in vivo and binding to the promoter in vitro are not dependent on the catalytic properties of M.EcoRII. Mobility shift experiments with C186S also revealed that it could bind either the promoter or unmethylated CCWGG sites, but not both. We conclude that the concentration of unmethylated CCWGG sites controls expression from the ecoRIIM promoter.

Analysis of nonmethylated GATC sites in the Escherichia coli chromosome and identification of sites that are differentially methylated in response to environmental stimuli

Seven GATC sites that are nonmethylated in logarithmic growth phase cells using glycerol as a carbon source were isolated from the Escherichia coli chromosome. Three of these GATC sites are located upstream of the operons gut, mtl, and ppiA, whereas DNA sequences adjacent to three other nonmethylated GATC sites are not homologous to previously identified genes. The seventh nonmethylated GATC site is located downstream of uspA. The protection of this site from DNA methylation requires leucine-responsive regulatory protein and is leucine responsive. The carbon source and the growth phase influenced the protection of the GATC site 5' of the ppiA gene. The other five sites were protected under all the environmental conditions examined.

Leucine-responsive regulatory protein and deoxyadenosine methylase control the phase variation and expression of the sfa and daa pili operons in Escherichia coli

The Escherichia coli operons daa and sfa encode F1845 and S pili, respectively. In this paper we show that the expression of these operons is under phase variation control at a transcriptional level. The transcription of both operons is dependent on the global regulator leucine-responsive regulatory protein (Lrp) and deoxyadenosine methylase (Dam). Lrp is required for methylation protection of two GATC sites located within conserved DNA sequences in the regulatory regions of these operons. These GATC sites are differentially methylated, establishing a methylation pattern which is characteristic of either the phase ON or phase OFF state. We also show that Lrp binds to the daa and sfa regulatory regions and that this binding is modulated by the methylation of the GATC sites. These results indicate that the phase variation of the daa and sfa operons is regulated by a mechanism involving differential binding of Lrp owing to methylation of GATC sites in the regulatory region, which is similar to the mechanism that controls phase variation of the pap operon.

Methylated cytosine at Dcm (CCATGG) sites in Escherichia coli: possible function and evolutionary implications

The frequency and distribution of methylated cytosine (5-MeC) at CCATGG (Dcm sites) in 49 E. coli DNA loci (207,530 bp) were determined. Principal observations of this analysis were: (1) Dcm frequency was higher than expected from random occurrence but lower than calculated with Markov chain analysis; (2) CCTGG sites were found more frequently in coding than in noncoding regions, while the opposite was true for CCAGG sites; (3) Dcm site distribution does not exhibit any identifiably regular pattern on the chromosome; (4) Dcm sites at oriC are probably not important for accurate initiation of DNA replication; (5) 5-MeC in codons was more frequently found in first than in second and third positions; (6) there are probably few genes in which the mutation rate is determined mainly by DNA methylation. It is proposed that the function of Dcm methylase is to protect chromosomal DNA from restriction-enzyme EcoRII. The Dcm methylation contribution to determine frequency of oligonucleotides, mutation rate, and recombination level, and thus evolution of the E. coli genome, could be interpreted as a consequence of the acquisition of this methylation.

A whole genome approach to in vivo DNA-protein interactions in E. coli

The increasingly rapid pace at which genomic DNA sequences are being determined has created a need for more efficient techniques to determine which parts of these sequences are bound in vivo by the proteins controlling processes such as gene expression, DNA replication and chromosomal mechanics. Here we describe a whole-genome approach to identify and characterize such DNA sequences. The method uses endogenous or artificially introduced methylases to methylate all genomic targets except those protected in vivo by protein or non-protein factors interfering with methylase action. These protected targets remain unmethylated in purified genomic DNA and are identified using methylation-sensitive restriction endonucleases. When the method was applied to the Escherichia coli genome, 0.1% of the endogenous adenine methyl-transferase (Dam methylase) targets were found to be unmethylated. Five foreign methylases were examined by transfection. Database-matched DNA sequences flanking the in vivo-protected Dam sites all fell in the non-coding regions of seven E. coli operons (mtl, cdd, flh, gut, car, psp and fep). In the first four operons these DNA sequences closely matched the consensus sequence that binds to the cyclic AMP-receptor protein. The in vivo protection at the Dam site upstream of the car operon was correlated with a downregulation of car expression, as expected of a feedback repressor-binding model.