Closing in on human methylation-the versatile family of seven-β-strand (METTL) methyltransferases

Abstract

Methylation is a common biochemical reaction, and a number of methyltransferase (MTase) enzymes mediate the various methylation events occurring in living cells. Almost all MTases use the methyl donor S-adenosylmethionine (AdoMet), and, in humans, the largest group of AdoMet-dependent MTases are the so-called seven-β-strand (7BS) MTases. Collectively, the 7BS MTases target a wide range of biomolecules, i.e. nucleic acids and proteins, as well as several small metabolites and signaling molecules. They play essential roles in key processes such as gene regulation, protein synthesis and metabolism, as well as neurotransmitter synthesis and clearance. A decade ago, roughly half of the human 7BS MTases had been characterized experimentally, whereas the remaining ones merely represented hypothetical enzymes predicted from bioinformatics analysis, many of which were denoted METTLs (METhylTransferase-Like). Since then, considerable progress has been made, and the function of > 80% of the human 7BS MTases has been uncovered. In this review, I provide an overview of the (estimated) 120 human 7BS MTases, grouping them according to substrate specificities and sequence similarity. I also elaborate on the challenges faced when studying these enzymes and describe recent major advances in the field.

Graphical Abstract

Figure 1.

The 7BS MTase reaction and fold. (A) The S-adenosylmethionine (AdoMet)-dependent MTase reaction. The MTase catalyses the transfer of a methyl group from AdoMet to the substrate, yielding S-adenosylhomocysteine (AdoHcy) and methylated substrate. (B) Topology of the canonical 7BS MTase fold. Key motifs involved in AdoMet (Motif I and Motif Post I) and substrate (Motif Post II) binding are indicated. The β-strands are shown in orange and numbered; α-helices are shown in green. (C) Three-dimensional structure of a typical 7BS MTase fold. A cartoon representation of the 7BS region (amino acids 68 -211) of the lysine-specific MTase METTL21A is shown. Colouring and numbering is as in (B). The structure (PDB: 4LEC) was visualized using PyMol (https://pymol.org/).

Figure 2.

Discovery, groupings and current status of human seven-β-strand methyltransferases (7BS MTases). The MTases have been placed in three groups according to their substrates, i.e. protein (red), DNA/RNA (blue) or small molecule (SM; green). Furthermore, characterized MTases are denoted as ‘established’, whereas uncharacterized MTases are denoted as either ‘tentative’ or ‘orphans’. For the tentative MTases, the substrate type (protein, DNA/RNA or SM) may be inferred from similarity to known MTases, while for the orphan MTases, the substrate type remains elusive. (A) Timeline for the discoveries of human 7BS MTases. The year of discovery indicates the time at which both the MTase activity and encoding gene had been uncovered. The current number of characterized MTases within each group is indicated by the number at the end of each curve. (B) Pie chart indicating the characterization status of the MTases as well as their distribution between the groups. Color code and groupings are as in (A), but with the tentative MTases indicated by pale colour. The orphan MTases are depicted in grey. The information used to generate the plots in (A) and (B) can be found in Supplementary Tables S1–S3. (C) Comparison of length distributions between 7BS MTases and SET-domain MTases. Information on the lengths of the 120 7BS MTases and 56 SET domain MTases in humans was obtained from UniProt.

Figure 3.

An inventory and overview of the human 7BS MTases. The MTases are indicated by their HGNC gene symbols, in some cases with alias symbols in parenthesis. In (A–C), established MTases are in bold print, whereas tentative MTases are in italics. In (A) and (B), the MTases have been placed into subgroups based on sequence similarity, and those that do not show appreciable similarity to others are designated as ‘unique’. (A) Subgroupings and substrates of protein MTases. Colors indicate the substrate types that are targeted by the MTases. PRMT, protein arginine MTase group; eEF1A-KMT, eukaryotic elongation factor 1α lysine MTase group; PCMT, protein isoaspartate (IsoAsp) MTase group; FAM173, Family With Sequence Similarity 173 group; HemK-like, similar to HemK from bacteria; NTMT, N-terminal MTase subgroup. ^#Note that CARNMT1, which first was shown to be a SM MTase, but was later established also as a protein MTase, is not counted as one of the 37 protein MTases, and thus placed in parenthesis; this is to avoid discrepancies with the numbers in Figure 1. (B) Subgroupings and products of DNA/RNA MTases. The DNA MTases are indicated by an asterisk (*). Colors indicate the products that are generated by the MTases. In most cases, the subgroups have been given names from bacterial (FtsJ) or yeast (Ime4, Nop1, Trm1, Trm2, Trm9, Trm61) homologues/orthologues, or the subgroup name indicates the methylated product formed. NSUN, NOL1/NOP2/SUN domain subgroup; DNMT, DNA MTase subgroup; Me-phos., 5′ methylphosphate-generating subgroup. (C) Unrooted phylogenetic tree of human small molecule (SM) MTases. MTases that display sequence similarity (beyond the generic 7BS motifs) are indicated by the same colour (blue, red, green or orange). (D) Orphan MTases. This group represents uncharacterized human 7BS MTases without tentative substrates.

Figure 4.

Products of 7BS MTase-catalysed reactions. Key products formed by 7BS MTase-mediated transfer of methyl groups (red or green) onto proteins (A), RNA/DNA (B) and small molecules (C). In (B), the abbreviations refer to the shown nucleobases (and not to RNA nucleosides, which is more common); this is because some of the methylated bases are discussed in the context of both DNA and RNA. In (C), the gene symbols of the enzymes responsible for the methylations are also indicated, i.e. AS3MT (arsenite MTase), ASMT (acetylserotonin O-MTase), CARNMT1 (carnosine N-MTase), COMT (catechol O-methyltransferase), COQ3 (ubiquinone biosynthesis O-MTase), COQ5 (ubiquinone biosynthesis MTase), GNMT (glycine N-MTase), NNMT (nicotinamide N-MTase), PNMT (phenylethanolamine N-MTase), TMT (thiol S-MTase).

Figure 5.

7BS MTases and cancer. (A) Timeline for the number of publications that contain either ‘methyltransferase’ and ‘methyltransferase AND cancer’ in their title or abstract (from PubMed). (B) Essentiality of 7BS MTases in human cancer cell lines assessed by using DepMap. The DepMap resource (https://depmap.org/) contains data from experiments where the essentiality of human genes was assessed by systematically knocking them out (using CRISPR) in a panel of ∼1100 human cancer cell lines, and then measuring cell viability. Based on these results, genes were categorized as either essential, non-essential, or selective, where the latter represents genes that are essential only in a subset of the cell lines. Also, the degree of essentiality was calculated using a CHRONOS score, where -1 and 0 represents the average of essential and non-essential genes, respectively. 117 of the 120 7BS MTases were analysed (data for ASMT, ASMTL, FBLL1 were not available). Supplementary Figure S1 shows a zoomed-in, higher resolution version of this panel, allowing viewing of the results for each individual MTase. (C) Groupwise presentation of the essentiality of the 7BS MTases.