DNA substrate specificity of pea DNA methylase

Analysis of overlapping cDNA clones specific for a putative second DNA methyltransferase-encoding gene in Arabidopsis thaliana

We have isolated and sequenced overlapping cDNA clones specific for a putative second DNA methyltransferase (MTase)-encoding gene (MTase11) from Arabidopsis thaliana (At) recently described as a genomic DNA fragment [Scheidt et al., Nucleic Acids Res. 22 (1994) 953-958]. The gene seems to be present as a single copy in the At genome and is transcribed into a 2.2-kb messenger detectable only in young seedlings. Using sequence comparison we found structural differences between the cDNA clones and the previously reported genomic fragment. The amino-acid sequence deduced from the 1.8-kb cDNA sequence shows the occurrence of the conserved motif number VI characteristic for m5C-MTases. Northern and Southern analysis detects no cross-hybridization with the originally described MTase-encoding At gene (MTase1) [Finnegan and Dennis, Nucleic Acids Res. 21 (1993) 2383-2388].

CG and CNG methyltransferases in plants

We have purified two distinct DNA methyltransferases from pea shoot tips and analysed their sequence specificity using synthetic oligodeoxyribonucleotide substrates and chemical sequencing methods. One methylates only CG target sequences, whereas the other methylates only CAG or CTG target sequences. We have found no evidence for methylation of the 5' cytosine in CCG target sequences either in vivo or in vitro. Using amino-acid sequence data, PCR-amplified fragments from conserved sequences and heterologous probes, we have isolated several cDNA clones that react with mRNA molecules of different sizes.

Characterization of an Arabidopsis thaliana DNA hypomethylation mutant

We have recently isolated two Arabidopsis thaliana DNA hypomethylation mutations, identifying the DDM1 locus, that cause a 70% reduction in genomic 5-methylcytosine levels [1]. Here we describe further phenotypic and biochemical characterization of the ddm1 mutants. ddm1/ddm1 homozygotes exhibited altered leaf shape, increased cauline leaf number, and a delay in the onset of flowering when compared to non-mutant siblings in a segregating population. Our biochemical characterization investigated two possible mechanisms for DNA hypomethylation. In order to see if ddm1 mutations affect DNA methyltransferase function, we compared DNA methyltransferase activities in extracts from wild-type and ddm1 mutant tissues. The ddm1 mutant extracts had as much DNA methyltransferase activity as that of the wild-type for both the CpI and CpNpG substrates suggesting that the DDM1 locus does not encode a DNA methyltransferase. Moreover, the ddm1 mutations did not affect the intracellular level of S-adenosylmethionine, the methyl group donor for DNA methylation. The possibility that the DDM1 gene product functions as a modifier of DNA methylation is discussed.

Sequence-specific hypomethylation of the tobacco genome induced with dihydroxypropyladenine, ethionine and 5-azacytidine

Higher plant DNA is methylated at CG and CNG targets. In this study we have investigated the tobacco methylation system in tissue culture using the methylation inhibitors 5-azacytidine (5-azaC), dihydroxypropyladenine (DHPA) and ethionine (Ethi), and methylation-sensitive restriction endonucleases HpaII, MspI, HhaI, EcoRII, ScrFI, and Fnu4HI. Surprisingly, CAG/CTG sequences, contrary to CG doublets and CCG/CGG triplets, appeared to be refractory to the inhibitory effect of 5-azaC. Thus 5-azaC cannot be considered a general inhibitor of DNA methylation in tobacco cells. On the other hand, DHPA, the inhibitor of S-adenosylhomocysteine (SAH) hydrolase, and Ethi caused hypomethylation of both CAG/CTG and CCG/CGG triplets but not of the CG doublets. The sensitivity of triplet-specific methylation to the inhibition of SAH hydrolase suggests the possibility that plant-specific DNA methylation at CNG targets might be modulated by alterations of the SAH/S-Adenosylmethionine ratio in plant cells.