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.Epigenetic regulation of gene expression by covalent modification of histone proteins and methylation of DNA controls development and disease processes 1 . Post-translational modification of histone proteins includes acetylation, phosphorylation and methylation. Many of these modifications occur on the N-terminal tails of the histone proteins that protrude from the nucleosome. Methylation of lysine residues in histone tails has been identified in histone H3 lysine residues 4, 9, 27 and 36; in histone H4 lysine 20; and in histone H1b lysine 25. Each of these methylations has different biological functions 1 .The first histone lysine methyltransferase was identified in 2000 (ref.2), and today about 30 different enzymes are known in different species 1 . Most protein lysine methyltransferases (PKMTs) contain a SET domain, which harbors the active center of the enzymes 3 . Here, we investigate the substrate sequence specificity of the human G9a PKMT, which is important for the euchromatic histone H3K9 methylation that is essential for early embryogenesis 4 , the propagation of imprints 5 and control of DNA methylation 6 . Knockout of G9a results in a decrease of global H3K9me1 and H3K9me2 levels 7 . In vitro G9a generates mainly H3K9me1 and H3K9me2 (ref. 8), as well as H3K9me3 after long incubation 9 . In contrast to the Dim-5 and Suv39H1 H3K9 methyltransferases, G9a methylates not only H3K9 but also H3K27 (ref. 10), which implicates different specificities in peptide recognition. To analyze the substrate specificity of PKMTs, we prepared peptide arrays on functionalized cellulose membranes using the first 21 residues of histone H3 as template 11 (Supplementary Methods online). The membranes were incubated with G9a in the presence of radioactively labeled [methyl-3 H]-S-adenosyl-L-methionine ( 3 H-AdoMet, 1), and the transfer of methyl groups to the immobilized peptides was detected by autoradiography ( Supplementary Fig. 1 online). To quantify the contribution of each amino acid to the recognition of the substrate and display it graphically, the discrimination factor of G9a at each position was calculated (Fig. 1a). The results showed that G9a interacts with H3 residues 6-11, which agrees with a report describing a heptapeptide of the histone H3 tail (TARKSTG) as the minimal substrate methylated by G9a (ref. 12). In addition to Lys9 (the target of methylation), Arg8 is the most important specificity determinant for G9a. Any other amino acid substituted at that position completely abolished the activity...

Escherichia coli multiple-deletion mutants were constructed to examine the lipid phosphatase genes. Ratio of cellular levels of undecaprenyl phosphate (UP) and undecaprenyl diphosphate (UPP) was determined using cells labeled with 14 C and measuring the radioactivities in these lipids. The labeled cells were obtained through feeding [ 14 C]isopentenyl diphosphate to an E. coli strain. The relative level of UP in the wild type strain W3110; in the YS1234 strain defective in ynbD, yeiU, ybjG, and pgpB; in the YS1235 strain defective in ynbD, yeiU, ybjG, and bacA; and in the YS1245 strain defective in ynbD, yeiU, pgpB, and bacA were 78.0% ± 3.5%, 74.7% ± 1.2%, 68.4% ± 6.8%, and 64.0% ± 7.5%, respectively. The quadruple mutant strain that possessed the wild-type bacA showed almost identical UP level as the wild type strain W3110, indicating that sufficient level of UPP phosphatse activity was conferred by a bacA product without the products of ynbD, yeiU, ybjG, and pgpB. However, the mutants defective in bacA showed a slight but significant (p < 0.01) decrease in the UP level.