A plant DNA-binding protein that recognizes 5-methylcytosine residues

Methyl-CpG-binding domain (MBD) proteins in plants

Cytosine methylation is the most prevalent epigenetic modification of plant nuclear DNA, which occurs in symmetrical CpG or CpNpG as well as in non-symmetrical contexts. Intensive studies demonstrated the central role played by cytosine methylation in genome organization, gene expression and in plant growth and development. However, the way by which the methyl group is interpreted into a functional state has only recently begun to be explored with the isolation and characterization of methylated DNA binding proteins capable of binding 5-methylcytosine. These proteins belong to an evolutionary conserved protein family initially described in animals termed methyl-CpG-binding domain (MBD) proteins. Here, we highlight recent advances and present new prospects concerning plant MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation.

Methyl-CpG-binding domain proteins in plants: interpreters of DNA methylation

The effect of DNA methylation on various aspects of plant cellular and developmental processes has been well documented over the past 35 years. However, the underlying molecular mechanism interpreting the methylation signal has only recently been explored with the isolation and characterization of the Arabidopsis methyl-CpG-binding domain (MBD) proteins. In this review, we highlight recent advances and present new models concerning Arabidopsis MBD proteins and their possible role in controlling chromatin structure mediated by CpG methylation.

AtMBD9: a protein with a methyl-CpG-binding domain regulates flowering time and shoot branching in Arabidopsis

The functional characterization of mammalian proteins containing a methyl-CpG-binding domain (MBD) has revealed that MBD proteins can decipher the epigenetic information encoded by DNA methylation, and integrate DNA methylation, modification of chromatin structure and repression of gene expression. The Arabidopsis genome has 13 putative genes encoding MBD proteins, and no specific biological function has been defined for any AtMBD genes. In this study, we identified three T-DNA insertion mutant alleles at the AtMBD9 locus, and found that all of them exhibited obvious developmental abnormalities. First, the atmbd9 mutants flowered significantly earlier than wild-type plants. The expression of FLOWERING LOCUS C (FLC), a major repressor of Arabidopsis flowering, was markedly attenuated by the AtMBD9 mutations. This FLC transcription reduction was associated with a significant decrease in the acetylation level in histone H3 and H4 of FLC chromatin in the atmbd9 mutants. Secondly, the atmbd9 mutants produced more shoot branches by increasing the outgrowth of axillary buds when compared with wild-type plants. The two known major factors controlling the outgrowth of axillary buds in Arabidopsis, auxin and the more axillary growth (MAX) pathway, were found not to be involved in producing this enhanced shoot branching phenotype in atmbd9 mutants, indicating that AtMBD9 may regulate a novel pathway to control shoot branching. This pathway is not related to FLC expression as over-expression of FLC in atmbd9-2 restored its flowering time to one similar to that of the wild type, but did not alter the shoot branching phenotype.

DNA Methylation in Plants

DNA in plants is highly methylated, containing 5-methylcytosine (m5C) and N6-methyladenine (m6A); m5C is located mainly in symmetrical CG and CNG sequences but it may occur also in other non-symmetrical contexts. m6A but not m5C was found in plant mitochondrial DNA. DNA methylation in plants is species-, tissue-, organelle- and age-specific. It is controlled by phytohormones and changes on seed germination, flowering and under the influence of various pathogens (viral, bacterial, fungal). DNA methylation controls plant growth and development, with particular involvement in regulation of gene expression and DNA replication. DNA replication is accompanied by the appearance of under-methylated, newly formed DNA strands including Okazaki fragments; asymmetry of strand DNA methylation disappears until the end of the cell cycle. A model for regulation of DNA replication by methylation is suggested. Cytosine DNA methylation in plants is more rich and diverse compared with animals. It is carried out by the families of specific enzymes that belong to at least three classes of DNA methyltransferases. Open reading frames (ORF) for adenine DNA methyltransferases are found in plant and animal genomes, and a first eukaryotic (plant) adenine DNA methyltransferase (wadmtase) is described; the enzyme seems to be involved in regulation of the mitochondria replication. Like in animals, DNA methylation in plants is closely associated with histone modifications and it affects binding of specific proteins to DNA and formation of respective transcription complexes in chromatin. The same gene (DRM2) in Arabidopsis thaliana is methylated both at cytosine and adenine residues; thus, at least two different, and probably interdependent, systems of DNA modification are present in plants. Plants seem to have a restriction-modification (R-M) system. RNA-directed DNA methylation has been observed in plants; it involves de novo methylation of almost all cytosine residues in a region of siRNA-DNA sequence identity; therefore, it is mainly associated with CNG and non-symmetrical methylations (rare in animals) in coding and promoter regions of silenced genes. Cytoplasmic viral RNA can affect methylation of homologous nuclear sequences and it maybe one of the feedback mechanisms between the cytoplasm and the nucleus to control gene expression.

Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins

The covalent modification of eukaryotic DNA by methylation of the 5' carbon of cytosine residues is frequently associated with transcriptional silencing. In mammals, a potential mechanism for transducing DNA methylation patterns into altered transcription levels occurs via binding of methyl-CpG-binding domain (MBD) proteins. Mammalian MBD-containing proteins bind specifically to methylated DNA and recruit chromatin-modifying complexes containing histone deacetylase activities. Sequence similarity searches reveal the presence of multiple proteins in plants containing a putative MBD. Outside of the MBD itself, there is no sequence relationship between plant and mammalian MBD proteins. The plant MBD proteins can be divided into eight classes based on sequence similarity and phylogenetic analyses of sequences obtained from two complete genomes (rice [Oryza sativa] and Arabidopsis [Arabidopsis thaliana]) and from maize (Zea mays). Two classes of MBD proteins are only represented in dicot species. The striking divergence of plant and animal MBD-containing proteins is in stark contrast to the amino acid conservation of DNA methyltransferases across plants, animals, and fungi. This observation suggests the possibility that while plants and mammals have retained similar mechanisms for the establishment and maintenance of DNA methylation patterns, they may have evolved distinct mechanisms for the interpretation of these patterns.

Extensive maternal DNA hypomethylation in the endosperm of Zea mays

A PCR-based genomic scan has been undertaken to estimate the extent and ratio of maternally versus paternally methylated DNA regions in endosperm, embryo, and leaf of Zea mays (maize). Analysis of several inbred lines and their reciprocal crosses identified a large number of conserved, differentially methylated DNA regions (DMRs) that were specific to the endosperm. DMRs were hypomethylated at specific methylation-sensitive restriction sites upon maternal transmission, whereas upon paternal transmission, the methylation levels were similar to those observed in embryo and leaf. Maternal hypomethylation was extensive and offers a likely explanation for the 13% reduction in methyl-cytosine content of the endosperm compared with leaf tissue. DMRs showed identity to expressed genic regions, were observed early after fertilization, and maintained at a later stage of endosperm development. The implications of extensive maternal hypomethylation with respect to endosperm development and epigenetic reprogramming will be discussed.

Characterization of Arabidopsis thaliana methyl-CpG-binding domain (MBD) proteins

Cytosine methylation at symmetrical CpG and CpNpG sequences plays a key role in the epigenetic control of plant growth and development; yet, the way by which the methylation signal is interpreted into a functional state has not been elucidated. In animals, the methylation signal is recognized by methyl-CpG-binding domain (MBD) proteins that specifically bind methylated CpG dinucleotides. In Arabidopsis thaliana, 12 putative MBD proteins were identified and classified into seven subclasses. Here, we characterized six MBD proteins representing four subclasses (II, III, IV, and VI) of the Arabidopsis MBD family. We found that AtMBD7 (subclass VI), a unique protein containing a double MBD motif, as well as AtMBD5 and AtMBD6 (subclass IV), bind specifically symmetrically methylated CpG sites. The MBD motif derived from AtMBD6, but not from AtMBD2, was sufficient for binding methylated CpG dinucleotides. AtMBD6 precipitated histone deacetylase (HDAC) activity from the leaf nuclear extract. The examined AtMBD proteins neither bound methylated CpNpG sequences nor did they display DNA demethylase activity. Our results suggest that AtMBD5, AtMBD6, and AtMBD7 are likely to function in Arabidopsis plants as mediators of the CpG methylation, linking DNA methylation-induced gene silencing with histone deacetylation.

Sequence-specific and methylation-dependent and -independent binding of rice nuclear proteins to a rice tungro bacilliform virus vascular bundle expression element

Nuclear proteins from rice (Oryza sativa) were identified that bind specifically to a rice tungro bacilliform virus promoter region containing a vascular bundle expression element (VBE). One set of proteins of 29, 33, and 37 kDa, present in shoot and cell suspension extracts but hardly detectable in root extracts, bound to a site containing the sequence AGAAGGACCAGA within the VBE, which also contains two CpG and one CpNpG potential methylation motifs. Binding by these proteins was determined to be cytosine methylation-independent. However, a novel protein present in all analyzed extracts bound specifically to the methylated VBE. A region of at least 49 nucleotides overlapping the VBE and complete cytosine methylation of the three Cp(Np)G motifs was required for efficient binding of this methylated VBE-binding protein (MVBP).

Characterization of carrot nuclear proteins that exhibit specific binding affinity towards conventional and non-conventional DNA methylation

DNA methylation is associated with transcriptional silencing in vertebrates and plants. In mammals, the effects of methylation are mediated by a family of methyl-CpG-binding proteins. In plants the mechanisms by which methylation represses transcription are still not clear. In this paper we describe protein factors in carrot nuclear extracts exhibiting specific affinities for conventional or non-conventional methylation acceptor sites. We characterized two classes of proteins: the first, dcMBPI (Daucus carota methylated DNA-binding protein 1), shows high affinity for sequences containing 5-methylcytosine; the second, dcMBP2 (Daucus carota methylated DNA-binding protein 2), efficiently complexes sequences containing 5-methylcytosine in both CpXpX and CpXpG trinucleotides and shows much lower affinity for 5-methyl CpG dinucleotides. Both dcMBP1 and dcMBP2 are abundant proteins differing in molecular weight and binding features. Their activities are modulated during carrot vegetative cell growth and somatic embryo development. This is the first time that, in either plants or mammals, proteins exhibiting specific binding affinities for conventional or non-conventional DNA methylation have been shown. Based on these results, the possibility that both the extent and the context of the methylation might contribute to modulate gene expression is discussed.

Demethylation and expression of methylated plasmid DNA stably transfected into HeLa cells

In vitro methylation at CG dinucleotides (CpGs) in a transfecting plasmid usually greatly inhibits gene expression in mammalian cells. However, we found that in vitro methylation of all CpGs in episomal or non-episomal plasmids containing the SV40 early promoter/enhancer (SV40 Pr/E) driving expression of an antibiotic-resistance gene decreased the formation of antibiotic-resistant colonies by only approximately 30-45% upon stable transfection of HeLa cells. In contrast, when expression of the antibiotic-resistance gene was driven by the Rous sarcoma virus long terminal repeat or the herpes simplex virus thymidine kinase promoter, this methylation decreased the yield of antibiotic-resistant HeLa transfectant colonies approximately 100-fold. The low sensitivity of the SV40 Pr/E to silencing by in vitro methylation was probably due to demethylation upon stable transfection. This demethylation may be targeted to the promoter and extend into the gene. By genomic sequencing, we showed that four out of six of the transfected SV40 Pr/E's adjacent Sp1 sites were hotspots for demethylation in the HeLa transfectants. High frequency demethylation at Sp1 sites was unexpected for a non-embryonal cell line and suggests that DNA demethylation targeted to certain aberrantly methylated regions may function as a repair system for epigenetic mistakes.

RNA-Mediated Virus Resistance: Role of Repeated Transgenes and Delineation of Targeted Regions

Resistance to cowpea mosaic virus (CPMV) in transgenic Nicotiana benthamiana plants is RNA mediated. In resistant CPMV movement protein (MP) gene-transformed lines, transgene steady state mRNA levels were low, whereas nuclear transcription rates were high, implying that a post-transcriptional gene-silencing mechanism is at the base of the resistance. The silencing mechanism can also affect potato virus X (PVX) RNAs when they contain CPMV MP gene sequences. In particular, sequences situated in the 3[prime] part of the transcribed region of the MP transgene direct elimination of recombinant PVX genomes. Remarkably, successive portions of this 3[prime] part, which can be as small as 60 nucleotides, all tag PVX genomes for degradation. These observations suggest that the entire 3[prime] part of the MP transgene mRNA is the initial target of the silencing mechanism. The arrangement of transgenes in the plant genome plays an important role in establishing resistance because the frequency of resistant lines increased from 20 to 60% when transformed with a transgene containing a direct repeat of MP sequences rather than a single MP transgene. Interestingly, we detected strong methylation in all of the plants containing directly repeated MP sequences. In sensitive lines, only the promoter region was found to be heavily methylated, whereas in resistant lines, only the transcribed region was strongly methylated.

Partial purification of a pea seed DNA-binding protein that specifically recognizes 5-methylcytosine

Previously, a DNA-binding protein (DBPm) was identified in plant nuclei that may mediate the effects of DNA methylation on chromatin structure and transcription. In the present report, DBPm was partially purified from germinated pea (Pisum sativum) seed nuclear extracts by DEAE-cellulose, phenylsepharose, heparin-sepharose chromatography, and preparative mobility shift on polyacrylamide gels. The purified activity showed a band at approximately 50 kD by sodium dodecyl sulfate-polyacrylamide gel electrophoresis as well as by Sephadex G100 chromatography, suggesting that DBPm is present as a monomer.

Effects of DNA methylation on DNA-binding proteins and gene expression

DNA methyltransferase is needed for normal development, perhaps because DNA methylation plays a part in the control of gene activity. It is clear that the methylation of promoters often leads to repression of transcription. Studies of the mechanism suggest that repression may either result from the direct effects of methylation on transcription factors, or may be indirectly caused by repressor proteins that bind to methylated DNA. Current evidence suggests that both mechanisms can be involved.

Characterization of DBPm, a plant protein that binds to DNA containing 5-methylcytosine

A protein (DBPm) has been isolated from nuclear extracts of soybean seeds, cauliflower florets, corn seed, wheat germ, and pea hypocotyl, seeds, apices, roots, and leaves that specifically binds to double-strand DNA containing 5-methylcytosine residues. In electrophoretic mobility shift assays, non-methylated duplex DNAs competed only slightly, while methylated DNAs were strong competitors. Specific binding still occurred after partial proteolysis of DBPm, but not after heating at 45 degrees C. By ultraviolet light-crosslinking and sodium dodecyl sulfate polyacrylamide gel electrophoresis and gel filtration, the size of pea seed DBPm was estimated to be in the range 70-90 kDa. From equilibrium binding studies the equilibrium constant for binding of pea seed DBPm to a 34 bp duplex deoxyoligonucleotide containing 12 5-methylcytosine residues was 1.2 x 10(9) M-1. The binding properties of DBPm make it a good candidate for a plant protein capable of mediating the effects of DNA methylation on the activity of some plant genes.

A broad bean cDNA clone encoding a DNA-binding protein resembling mammalian CREB in its sequence specificity and DNA methylation sensitivity

A plant cDNA has been cloned that encodes a DNA-binding protein displaying a nucleotide (nt) sequence specificity similar to that of the mammalian cyclic AMP response element-binding protein/activating transcription factor (CREB/ATF) family of mammalian proteins. This cDNA was cloned in Escherichia coli from a broad bean (Vicia faba) cDNA expression library using a recognition site probe. The deduced amino acid (aa) sequence of the recombinant cDNA-encoded protein, called VBP1, has a basic region adjacent to a leucine zipper motif, of the type seen in the DNA-binding domains of many eukaryotic DNA-binding proteins, including mammalian CREB/ATF. Although this aa sequence has homology to regions of deduced aa sequences of other cloned plant cDNAs, it is distinct in both the derived primary structure and in its nt sequence specificity. VBP1, as well as proteins in nuclear extracts of V. faba with similar nt sequence specificity, have their binding to DNA suppressed more than tenfold by cytosine methylation at the CREB/ATF consensus sequence.

Increasing the activity of affinity-purified DNA-binding proteins by adding high concentrations of nonspecific proteins

A large decrease in the activity of two sequence-specific DNA-binding proteins implicated in transcription control was seen when these were affinity purified and assayed under standard conditions in electrophoretic mobility shift assays. Increasing the concentration of bovine serum albumin in the reaction mixtures from 0.1 to 5 mg/ml stimulated the DNA-binding activity of these affinity-purified proteins, human CREB (cyclic AMP response element binding protein) and MDBP (methylated DNA-binding protein), approximately 5-to more than 20-fold. In the case of affinity-purified MDBP, adding back the affinity flow-through fraction to the assay mixture gave similar extents of stimulation at much lower final protein concentrations. The specific DNA-binding activity of the affinity-purified CREB, but not that of MDBP, was also increased by adding a nonionic detergent to the binding reaction buffer although not as much. The large increase in the amount of MDBP.DNA complex seen upon supplementation of the affinity-purified MDBP with the affinity flow-through fraction or 5 mg/ml of BSA was shown to be due to stimulation, by nonspecific proteins, of specific complex formation and not to prevention of activity losses by adsorption or denaturation during the assay.

CpG methylation inhibits binding of several sequence-specific DNA-binding proteins from pea, wheat, soybean and cauliflower

To elucidate how methylation of specific sites in plant DNA might control transcription, we examined the effect of DNA methylation at CpG sequences on the binding of plant nuclear factors to an oligonucleotide duplex containing the consensus sequence for mammalian CREB (cAMP response element binding protein). CREB is part of the ATF (activating transcription factor) family of mammalian proteins specifically binding to 5'-TGACGTCA-3' and related sequences. Proteins recognizing the CREB-specific ligand were identified in nuclear extracts of pea seeds, wheat germ, cauliflower, and soybean leaves using electrophoretic mobility shift assays. Cytosine methylation inhibited binding of this protein in all these extracts, and so this sequence-specific DNA-binding activity is referred to as methylation-inhibited binding protein 1 (MIB-1). Sites somewhat similar to that of the CREB ligand are found in the upstream regions of a wheat histone H3 gene and tomato and pea ribulose 1,5-bisphosphate carboxylase genes. These sites were bound preferentially by distinct proteins that may be related to the previously described plant proteins HBP-1, HSBF, ASF-1, or GBF. Methylation of cytosine residues at these sites and at a site for MIB-1 located upstream of a soybean proline-rich protein gene also reduced specific binding with all the nuclear extracts tested. Similarly, substitution of the central CpG dinucleotide with TpG decreased binding.

Three MDBP sites in the immediate-early enhancer-promoter region of human cytomegalovirus

MDBP, a mammalian sequence-specific DNA-binding protein, was found to recognize two sites in the major immediate-early (IE) enhancer of human cytomegalovirus. The recognition sequence for MDBP at each of these sites was localized to 14 bp by studying the effects of limited G methylation, depurination, depyrimidination, or deoxyribose modification on the ability of these sites to bind to MDBP. In addition to the two high-affinity MDBP sites in the enhancer, one low-affinity MDBP site was detected 5 bp after the transcription initiating residue of this IE transcription unit. The possible biological significance of the two enhancer MDBP sites and the downstream MDBP site is discussed.