Analysis of the substrate specificity of the Dim-5 histone lysine methyltransferase using peptide arrays

Coordinated chromatin control: structural and functional linkage of DNA and histone methylation

One of the most fundamental questions in the control of gene expression in mammals is how epigenetic methylation patterns of DNA and histones are established, erased, and recognized. This central process in controlling metazoan gene expression includes coordinated covalent modifications of DNA and its associated histones. This review focuses on recent developments in characterizing the functional links between the methylation status of the DNA and of two particularly important histone marks. Mammalian DNA methylation is intricately connected to the presence of unmodified lysine 4 and methylated lysine 9 residues in histone H3. An interconnected network of methyltransferases, demethylases, and accessory proteins is responsible for changing or maintaining the modification status of specific regions of chromatin. The structural and functional interactions among members of this network are critical to processes that include imprinting and differentiation, dysregulation of which is associated with disorders ranging from inflammation to cancer.

DNA methylation and the formation of heterochromatin in Neurospora crassa

Studies of the control and function of DNA methylation in Neurospora crassa have led to a greater understanding of heterochromatin formation. DNA methylation in Neurospora is dependent on trimethylation of histone H3 lysine 9 (H3K9me3) by the histone methyltransferase, DIM-5. The linkage between these two methyl marks is facilitated by heterochromatin protein 1 (HP1), which serves as an adapter protein. HP1 binds to the H3K9me3 and recruits the DNA methyltransferase, DIM-2. Although HP1 links H3K9me3 to DNA methylation, it also serves to recruit the DNA methylation modifier complex to the edges of heterochromatin regions, where it serves to limit the spreading of the heterochromatin by countering H3K9me3.

Chemical approaches for studying histone modifications

Histones form the protein core around which genomic DNA is wrapped in eukaryotic chromatin. Numerous genetic studies have established that the structure and transcriptional state of chromatin are closely related to histone post-translational modifications. Further elucidation of the precise mechanistic roles for individual histone modifications requires the ability to isolate and study homogeneously modified histones. However, the highly heterogeneous nature of histone modifications in vivo poses a significant challenge for such studies. Chemical tools that have enabled biochemical and biophysical studies of site-specifically modified histones are the focus of this minireview.

Structural biology of human H3K9 methyltransferases

SET domain methyltransferases deposit methyl marks on specific histone tail lysine residues and play a major role in epigenetic regulation of gene transcription. We solved the structures of the catalytic domains of GLP, G9a, Suv39H2 and PRDM2, four of the eight known human H3K9 methyltransferases in their apo conformation or in complex with the methyl donating cofactor, and peptide substrates. We analyzed the structural determinants for methylation state specificity, and designed a G9a mutant able to tri-methylate H3K9. We show that the I-SET domain acts as a rigid docking platform, while induced-fit of the Post-SET domain is necessary to achieve a catalytically competent conformation. We also propose a model where long-range electrostatics bring enzyme and histone substrate together, while the presence of an arginine upstream of the target lysine is critical for binding and specificity.

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Catalytic turnover-based phage selection for engineering the substrate specificity of Sfp phosphopantetheinyl transferase

We report a high-throughput phage selection method to identify mutants of Sfp phosphopantetheinyl transferase with altered substrate specificities from a large library of the Sfp enzyme. In this method, Sfp and its peptide substrates are co-displayed on the M13 phage surface as fusions to the phage capsid protein pIII. Phage-displayed Sfp mutants that are active with biotin-conjugated coenzyme A (CoA) analogues would covalently transfer biotin to the peptide substrates anchored on the same phage particle. Affinity selection for biotin-labeled phages would enrich Sfp mutants that recognize CoA analogues for carrier protein modification. We used this method to successfully change the substrate specificity of Sfp and identified mutant enzymes with more than 300-fold increase in catalytic efficiency with 3'-dephospho CoA as the substrate. The method we developed in this study provides a useful platform to display enzymes and their peptide substrates on the phage surface and directly couples phage selection with enzyme catalysis. We envision this method to be applied to engineering the catalytic activities of other protein posttranslational modification enzymes.

Protein phosphatase PP1 is required for normal DNA methylation in Neurospora

Covalent modifications of histones integrate intracellular and extracellular cues to regulate the genome. H3 Lys 9 methylation (H3K9me) can direct heterochromatin formation and DNA methylation, while phosphorylation of H3 Ser 10 (H3S10p) drives gene activation and chromosome condensation. To examine the relationship between H3S10p, H3K9me, and DNA methylation in Neurospora crassa, we built and tested mutants of the putative H3S10 phosphatase, PP1. A PP1-impaired mutant showed increased H3S10p and selective reduction of methylation of H3K9 and DNA. Similarly, amino acid substitutions of H3S10 abolished methylation of H3K9 and DNA. Thus, H3S10 dephosphorylation by PP1 is required for DNA methylation of some loci.

Putting the pieces together: histone H2B ubiquitylation directly stimulates histone H3K79 methylation

Employing an in vitro reconstitution approach, McGinty et al. studied the mechanism of stimulation of the Dot1-catalysed histone H3 methylation at Lys79 by histone H2B ubiquitylation at Lys120. To generate nucleosome particles that carry the ubiquitylation at Lys120, they chemically connected three polypeptides-the main parts of histone H3 and ubiquitin expressed in bacteria and a branched synthetic peptide. Using the semisynthetically produced nucleosome substrates and purified Dot1 enzyme, they showed that Dot1 is directly stimulated by the ubiquitylation, thus ruling out the need for further protein factors to mediate the effect.

Peptide arrays for enzyme profiling

Enzymes are key molecules in signal transduction pathways. However, only a small fraction of more than 500 predicted human kinases, 250 proteases and 250 phosphatases is characterized so far. Peptide microarray-based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. Additionally, patterns of enzymatic activities could be used to fingerprint the status of cells or organisms. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimization of enzyme substrates. A comprehensive overview regarding enzyme profiling using peptide microarrays is presented with special focus on assay principles.

Specificity of protein lysine methyltransferases and methods for detection of lysine methylation of non-histone proteins

Post translational modification of histone proteins including lysine methylation is an important epigenetic mark, essential for gene regulation and development. Recently, several examples of lysine methylation of non-histone proteins have been discovered suggesting that this is a common post-translational modification for regulation of protein activity. Here, we review assays for the detection of protein methylation based on mass spectrometry, radiolabel and immunological approaches using protein and peptide substrates including application of SPOT peptide arrays. Candidates for new methylation targets of protein methyltransferases can be predicted using the specificity of the enzyme and protein interaction data.

Protein lysine methyltransferase G9a acts on non-histone targets

By methylation of peptide arrays, we determined the specificity profile of the protein methyltransferase G9a. We show that it mostly recognizes an Arg-Lys sequence and that its activity is inhibited by methylation of the arginine residue. Using the specificity profile, we identified new non-histone protein targets of G9a, including CDYL1, WIZ, ACINUS and G9a (automethylation), as well as peptides derived from CSB. We demonstrate potential downstream signaling pathways for methylation of non-histone proteins.