Uncovering the Human Methyltransferasome

Abstract

We present a comprehensive analysis of the human methyltransferasome. Primary sequences, predicted secondary structures, and solved crystal structures of known methyltransferases were analyzed by hidden Markov models, Fisher-based statistical matrices, and fold recognition prediction-based threading algorithms to create a model, or profile, of each methyltransferase superfamily. These profiles were used to scan the human proteome database and detect novel methyltransferases. 208 proteins in the human genome are now identified as known or putative methyltransferases, including 38 proteins that were not annotated previously. To date, 30% of these proteins have been linked to disease states. Possible substrates of methylation for all of the SET domain and SPOUT methyltransferases as well as 100 of the 131 seven-␤-strand methyltransferases were surmised from sequence similarity clusters based on alignments of the substrate-specific domains. Molecular & Cellular Proteomics 10: 10.1074/mcp.M110.000976, 1-12, 2011.A significant percentage of proteins across all organisms are enzymes that catalyze the transfer of a methyl group from the cofactor S-adenosylmethionine to a substrate (1-5). In yeast, these proteins make up about 1.2% of all gene products (6, 7). The ability of methyltransferases to use a variety of different substrates, including RNA, DNA, lipids, small molecules, and proteins, is responsible for their diverse roles in different biological pathways (1-3). Methyltransferases have been shown to be essential in epigenetic control, lipid biosynthesis, protein repair, hormone inactivation, and tissue differentiation (8 -14). The identification of new enzymes may allow the delineation of additional pathways and modes of regulation as well as increase our understanding of S-adenosylmethionine metabolism.Although there are hundreds of known substrates for these reactions, methyltransferases are found in a small number of distinct structural arrangements that are used to classify them into superfamilies (2,3,5,6,15). Proteins in each superfamily also share conserved amino acid sequences. The seven-␤-strand superfamily (also referred to as "Class I" methyltransferases) is the most abundant. These proteins catalyze a wide array of substrates and feature a Rossmann-like structural core (2,3,5,6,15). The SPOUT methyltransferase superfamily contains a distinctive knot structure and methylates RNA substrates (16). SET domain methyltransferases catalyze the methylation of protein lysine residues with histones and ribosomal proteins as major targets (17)(18)(19). Smaller superfamilies with at least one three-dimensional structure available include the precorrin-like methyltransferases (20), the radical SAM 1 methyltransferases (21, 22), the MetH activation domain (23), the Tyw3 protein involved in wybutosine synthesis (24), and the homocysteine methyltransferases (25-27). Lastly, an integral membrane methyltransferase family has been defined by sequence alone where no three-dimensional structure is yet available (28,29).Ad...

The ribosome: A hot spot for the identification of new types of protein methyltransferases

“…In the first place, the combination of bioinformatics and the biology of Saccharomyces cerevisiae have allowed an approach to identify methylated sites in yeast proteins (23,24,29,30). Bioinformatic analyses have allowed for the identification of open reading frames for candidate methyltransferases from genomic DNA sequences both of the major seven beta-strand family and of the SET domain, SPOUT, and other structural families (31)(32)(33)(34)(35). Importantly, the ability of S. cerevisiae to transport Sadenosylmethionine across its plasma membrane (36) allows for radiolabeling of methylated proteins in intact cells and for their detection at sub-femtomole levels (see below).…”

Lysine methylation of VCP by a member of a novel human protein methyltransferase family

“…Protein methylation can be dynamic and serve regulatory purposes, or it can be static and function as an expansion of the amino-acid repertoire. Most MTases use S-adenosyl methionine (SAM) as methyl donor, and the human genome encodes over 200 putative SAM-dependent MTases, most of which remain uncharacterized 2 . The majority of these MTases belongs to either the SET domain family or to the seven β-strand superfamily, also designated 'Class I MTases' 2,3 .…”

“…Most MTases use S-adenosyl methionine (SAM) as methyl donor, and the human genome encodes over 200 putative SAM-dependent MTases, most of which remain uncharacterized 2 . The majority of these MTases belongs to either the SET domain family or to the seven β-strand superfamily, also designated 'Class I MTases' 2,3 . Most characterized lysine-specific MTases are SET domain proteins acting primarily on histones, but a few lysine-specific protein MTases have also been found in Class I.…”

An enzyme-coupled high-throughput assay for screening RNA methyltransferase activity inE. Colicell lysate

“…1 The different representatives of this class of enzymes are responsible for the methylation of very diverse substrates such as nucleic acids, lipids, proteins or small molecules and thus involved in numerous important metabolic pathways.…”