Cleavage of DNA by HaeII is inhibited by the presence of 5-methylcytosine at the second cytosine within the recognition sequence

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[Isolation, purification and properties of restrictase and methylase BstN1 from Bacillus stearothermophilus]

Restriction-methylation enzymes BstN1 from Bacillus stearothermophilus were isolated and purified. These enzymes are related to a new class of restriction-methylation enzymes of the second type, whose modifying component is N4-cytosine-DNA-methylase. Both enzymes recognize the DNA sequence CC(A/T)GG. Restrictase BstN1 is a protein made up of one subunit with a molecular mass of 25 kDa. The molecular mass of native DNA-methylase BstN1 is about 55 kDa. The temperature optima for restrictase and methylase BstN1 are around 60 degrees C. Possible uses of BstN1 restriction-methylation enzymes for the analysis of cytosine methylation in bacterial and higher plant DNA are discussed.

DNA methylation of the Ha-ras-1 oncogene in neoplastic cells

The DNA methylation pattern of the human Ha-ras-1 oncogene and the levels of specific mRNA have been analysed in established tumor cell lines and in surgical biopsies. In long-term cultures, the Ha-ras-1 gene is hypomethylated at its 5' end and highly methylated at its 3' portion. The GCGC sites at the 5' end have been shown to become methylated only when E. Coli HhaI methylase is added to isolated DNA, while they remain unmethylated when the enzyme is added to chromatin. These data indicate that the 5' portion of this protooncogene is maintained physiologically unmethylated, possibly because it is necessary for gene transcription. Along the same line of evidence, when levels of mRNA and methylation of the gene were comparatively analysed in breast tumors and autologous normal mammary tissue, no appreciable differences in the degree of methylation were found despite significant differences in mRNA content. These findings show that the levels of Ha-ras- mRNA are independent of the DNA methylation state.

Involvement of E. coli dcm methylase in Tn3 transposition

The effects of DNA methyltransferases on Tn3 transposition were investigated. The E. coli dam (deoxyadenosine methylase) gene was found to have no effect on Tn3 transposition. In contrast, Tn3 was found to transpose more frequently in dcm+ (deoxycytosine methylase) cells than in dcm- mutants. When the EcoRII methylase gene was introduced into dcm- cells (E. coli strain GM208), the frequency of Tn3 transposition in GM208 was dramatically increased. The EcoRII methylase recognizes and methylates the same sequence as does the dcm methylase. These results suggest that deoxycytosine methylase modified DNA may be a preferred target for Tn3 transposition. Experiments were also performed to determine whether the Tn3 transposase was involved in DNA modification. Plasmid DNA isolated from dcm- E. coli containing the Tn3 transposase gene was susceptible to ApyI digestion but resistant to EcoRI digestion, suggesting that Tn3 transposase modified the dcm recognition sequence. In addition, restriction enzymes TaqI, AvaII, BglI and HpaII did not digest this DNA completely, suggesting that the recognition sequences of TaqI, AvaII, BglI and HpaII were modified by Tn3 transposase to a certain degree. The type(s), the extent and mechanism(s) of this modification remain to be investigated.

Purification of a DNA methyltransferase from Bacillus natto B3364

An S-adenosyl-L-methionine:DNA-methyltransferase, termed M.BnaI, was purified from Bacillus natto B3364 strain by successive column chromatography. The molecular weight determined by gel filtration was 37 kDa for M.BnaI. Analysis of methyltransferase by sodium dodecyl sulfate-polyacrylamide gel electrophoresis showed correspondence of the M.BnaI activity with one protein band at a molecular weight of 35 kDa. Sequencing of pUC19 DNA methylated with M.BnaI showed the cytosine-5 methylation in the BnaI recognition sequence GGAT decreases CC at the position indicated by the arrow.

Methylation in eucaryotes influences the repair of G/T and A/C DNA basepair mismatches

Although methylation of DNA at some sites regulates gene expression, 5mC at many sites does not appear to have any effect. We present evidence that hemimethylation at many different sites can act as a discrimination signal in mismatch repair. Deamination of 5mC in a symmetrically methylated doublet CpG yields the mismatched base pair T/G in a hemi-methylated doublet pair. Because both bases in the mismatched pair are normal constituents of DNA, identifying the incorrect base is problematic. The only apparent distinction of the two is the methylation on the strand opposite the deamination event. Using available methylases we have produced hemi-methylated SV40 DNAs that are mismatched at a single T/G or A/C basepair in a sequence that mimics the lesion resulting from the deamination of a 5mCpG. Methylation at the adjacent cytosine results in the replacement of the T much more frequently than when no methylation is present in the heteroduplex. Cytosine methylation at sites farther removed from the mismatch is equally effective in replacing the incorrect T at the mismatch. Although methylation in vertebrates is almost exclusively on cytosine in the doublet CpG, methylation of cytosines in other doublets, as well as methylation of adenosine, also act as strand discrimination signals. Perhaps some of the excess methylation in vertebrate DNAs may serve to direct mismatch repair.

In vitro DNA cytosine methylation of cis-regulatory elements modulates c-Ha-ras promoter activity in vivo

The effect of DNA cytosine methylation on promoter activity was assessed using a transient expression system employing pHrasCAT. This 551 bp Ha-ras-1 gene promoter region is enriched with 84 CpG dinucleotides, six functional GC boxes, and is prototypic of many genes possessing CpG islands in their promoter regions. Bacterial modification enzymes HhaI methyl transferase (MTase) and HpaII MTase, alone or in combination with a human placental DNA methyltransferase (HP MTase) that methylates CpG sites in a generalized manner, including asymmetric elements such as GC box CpG's, were used to methylate at different types of sites in the promoter. Methylation of HhaI and HpaII sites reduced CAT expression by approximately 70%-80%, whereas methylation at generalized CpG sites with HP MTase inactivated the promoter by greater than 95%. The inhibition of H-ras promoter activity was not attributable to methylation-induced differences in DNA uptake or stability in the cell, topological form of the plasmid, or methylation effects in non-promoter regions.

Inhibition of rat growth hormone promoter activity by site-specific DNA methylation

The effect of methylation on rat growth hormone (rGH) promoter activity was determined in GH3 cells by measuring rGH-Neo and rGH-CAT fusion gene expression with or without prior in vitro treatment with the site-specific DNA methyltransferases, M-BsuE and M-HhaI. To assay for rGH-promoter-specific effects of DNA methylation, RSV-Neo and RSV-CAT activities with or without M-BsuE, M-HhaI and M-HpaII treatment were measured in parallel cultures of GH3 cells. GH1-Neo and RSV-Neo fusion gene expression was inhibited by in vitro methylation from 44 to 83% as measured by the number of Geneticin-resistant GH3 cell colonies. Methylation of the GH1 promoter by M-BsuE exhibited some selective inhibition of Neo expression as determined by colony numbers, although extensive methylation of non-promoter DNA in GH1-Neo and RSV-Neo by M-HhaI and M-HpaII also inhibited Neo expression. Southern blot analysis of genomic DNA isolated from the Geneticin-resistant GH3 cells indicated that Geneticin-resistance was accompanied by demethylation of the BsuE (ThaI) sites in stably incorporated GH1-Neo DNA but not RSV-Neo DNA. Transient expression of the CAT gene in GH3 cells was selectively inhibited by 60% upon methylation of two BsuE (ThaI) sites in the GH1 promoter of GH1-CAT by M-BsuE. The data demonstrate, for the first time, to our knowledge, a direct effect of DNA methylation on the activity of the rat growth hormone promoter.

Evolution of type II DNA methyltransferases. A gene duplication model

On the basis of consensus sequences, which had previously been defined for two groups of closely related cytosine-specific and adenine-specific DNA methyltransferases, homologies can be detected that indicate a common origin for these proteins. Intramolecular comparisons of several of these enzymes reveal homology relationships, which suggests that gene duplication is a phylogenetic principle in the evolution of the Mtases. One or two duplications of an ancestral gene encoding a 12,000 to 16,000 Mr protein, followed by divergent evolution, may have led to very different protein structures and could explain the differences in amino acid sequences, molecular weights and biochemical properties. Intermolecular and intramolecular homologies were also recognized in type II restriction endonucleases, suggesting a very similar evolutionary pathway.

Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains

Comparisons of the amino acid sequences of m5C DNA methyltransferases (Mtases) from 11 prokaryotes and one eukaryote reveal a very similar organization. Among all the enzymes one can distinguish highly conserved "core" sequences and "variable" regions. The core sequences apparently mediate steps of the methylation reaction that are common to all the enzymes. The major variable region has been shown in our previous studies on multispecific phage Mtases to contain the target-recognizing domains (TRDs) of these enzymes. Here we have compared the amino acid sequences of various TRDs from phage Mtases. This has revealed the presence of both highly conserved and variable amino acids. We postulate that the conserved residues represent a "consensus" sequence defining a TRD, whereas the specificity of the TRD is determined by the variable residues. We have observed similarity between this consensus sequence and sequences in the variable region of the monospecific Mtases. We predict that the regions thus identified represent part of the TRDs of monospecific Mtases.

In situ methylation of human chromosomes with methylase-AluI

A method for in situ DNA methylation with the prokaryotic methylase AluI has been developed for use on fixed human chromosomes. Incorporation of methyl groups into the chromosomal DNA has been shown by autoradiography using a labeled substrate. The methylation prevents the digestion of chromosomal DNA by AluI, allowing direct visualization of clusters of nonmethylated AGCT targets along the human complement.

The 5'-GGATCC-3' cleavage specificity of BamHI is increased to 5'-CCGGATCCGG-3' by sequential double methylation with M.HpaII and M.BamHI

Site-specific DNA methylation is known to block cleavage by a number of restriction endonucleases. We show that methylation at 'non-canonical' DNA modification sites can also block methylation by five of 13 DNA methyltransferases (MTases) tested. Furthermore, MTases and endonucleases that recognize the same nucleotide sequence can differ in their sensitivity to non-canonical methylation. In particular, BamHI endonuclease can cut 5'-GGATCm5C efficiently, whereas M.BamHI cannot methylate this modified sequence. Methyltransferase/endonuclease pairs which differ in their sensitivity to non-canonical methylation can be exploited to generate rare DNA cleavage sites. For example, we show that M.HpaII, M.BamHI, and BamHI can be used sequentially in a three-step procedure to specifically cleave DNA at the 10-bp sequence 5'-CCGGATCCGG. Several highly selective DNA cutting strategies are made possible by these sequential double methylation-blocking reactions.

Cytosine methylation as an effector of right-handed to left-handed DNA structural transitions

Cytosine methylation has energetic and structural influences on left-handed Z-DNA formation in supercoiled plasmids. The restriction and modification enzymes from Haemophilus haemolyticus (HhaI and M.HhaI) provide a system to locate and analyze small segments of Z-DNA in large supercoiled plasmids. An approach is outlined that uses M.HhaI as an in vivo conformational probe for the detection of unusual DNA structures in a living cell. Also, characteristic features of the M.HhaI gene and protein are discussed.

DNA methyltransferase of Bacillus subtilis Marburg: purification, properties and further evidence of specificity

Bacillus subtilis Marburg strain displays DNA methyltransferase activity. This enzyme, M.BsuM, methylates cytosine in the sequence 5'-YTCGAR-3' (Y = pyrimidine; R = purine). M.BsuM was purified from the exponentially growing cells of B. subtilis 168M. This enzyme (45 +/- 1 kDa) is monomeric and recognizes only double-stranded DNA. It is inhibited partially by Mg2+, Mn2+ ions and spermidine and almost totally by sodium dodecyl sulfate, urea and agarose. This enzyme methylates specifically the three methylatable sites of the plasmid pBM3. Relaxation of specificity ('star' activity) was observed in the presence of organic solvents. A very low amount of M.BsuM was obtained in the standard Marburg strain. To obtain sufficient enzyme attempts are being made to clone the M.BsuM gene in Escherichia coli by using a constructed plasmid (pBM14) vector. Only one transformant containing a 3-kb insert and showing a low level of expression, was obtained.

Cloning and analysis of the HaeIII and HaeII methyltransferase genes

The HaeIII methyltransferase (MTase) gene from Haemophilus aegyptius (recognition sequence: 5'-GGCC-3') was cloned into Escherichia coli in the plasmid vector pBR322. The gene was isolated on a single EcoRI fragment and on a single HindIII fragment. Clones carrying additional adjacent fragments were found to code also for the HaeII restriction endonuclease and HaeII modification MTase (recognition sequence: 5'-PuGCGCPy-3'). The sequence of the HaeIII modification gene was determined. The inferred amino acid sequence of the protein was found to share extensive similarity with other sequenced m5C-MTases. The central 'non-conserved' region of the M.HaeIII MTase, thought to form the nucleotide sequence-specificity domain, is almost identical to that of the M.BsuRI, M.BspRI and M.NgoPII MTases, which also recognize the sequence 5'-GGCC-3'.

Reduced methyl group acceptance of 1-beta-D-arabinofuranosylcytosine-containing DNA polymers

Previous studies have shown that 1-beta-D-arabinofuranosylcytosine (ara-C) can induce differentiation of various malignant cells and that DNA methylation patterns become altered under ara-C treatment of those cells. The aim of this study was to investigate whether this influence on DNA methylation is caused by a direct effect of DNA-incorporated ara-C molecules on nuclear DNA methylase. For this reason, we constructed various ara-C-substituted DNA polymers and used them as substrates for highly purified eukaryotic DNA methylase isolated from murine P815 mastocytoma cells. The ara-C incorporation into DNA polymers was measured by either an ara-C-specific radioimmunoassay or by use of radioactive-labelled ara-C during the synthesis of those polymers. We found an inverse correlation between the level of ara-C substitution of the DNA polymers and their methyl group acceptance. Kinetic experiments performed with ara-C-modified DNA polymers pointed out that the mode of action of DNA methylase remains unaltered. DNA methylase is neither detached nor fixed at an ara-C site, but is somehow hindered in its enzymatic activity, probably by slowing down the walking mechanism. Hence, the previously observed hypermethylation of DNA of some eukaryotic cells, propagated in the presence of ara-C, is apparently not due to a direct effect of DNA-incorporated ara-C molecules on endogenous DNA methylase.