Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor

Abstract

S-adenosylmethionine (SAM) is an essential metabolite that acts as a cofactor for most methylation events in the cell. The N-methyladenosine (mA) methyltransferase METTL16 controls SAM homeostasis by regulating the abundance of SAM synthetase MAT2A mRNA in response to changing intracellular SAM levels. Here we present crystal structures of METTL16 in complex with MAT2A RNA hairpins to uncover critical molecular mechanisms underlying the regulated activity of METTL16. The METTL16-RNA complex structures reveal atomic details of RNA substrates that drive productive methylation by METTL16. In addition, we identify a polypeptide loop in METTL16 near the SAM binding site with an autoregulatory role. We show that mutations that enhance or repress METTL16 activity in vitro correlate with changes in MAT2A mRNA levels in cells. Thus, we demonstrate the structural basis for the specific activity of METTL16 and further suggest the molecular mechanisms by which METTL16 efficiency is tuned to regulate SAM homeostasis.

Functions of N6-methyladenosine and its role in cancer

“…METTL16 binds a subset of mRNAs and methylates long noncoding RNA (lncRNA) and U6 small nuclear RNA (U6 snRNA) [59,60]. The UACAGAGAA sequence is required for METTL16-mediated-methylation and the Nterminal module of METTL16 is essential for RNA binding [61,62].…”

N6-Adenosine Methylation in RNA and a Reduced m3G/TMG Level in Non-Coding RNAs Appear at Microirradiation-Induced DNA Lesions

“…Moreover, METTL16-mediated modification at the 5 splice sites is considered as an important component of the splicing machinery [20]. Moreover, Doxtader et al showed that METTL16 regulates a key metabolite of homeostasis, S-adenosylmethionine SAM, which is a well-known DNA methylation cofactor [21].…”

Identification of m6A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline

“…Therefore, in addition to ensuring accurate quantification of starting material via the methods outlined in our protocol, we also highly encourage the use of multiple replicates when starting RNA material is limited to gain confidence in the identified m 6 A residues. Further, while the majority of m 6 A deposition in humans occurs via the METTL3/METTL14 writer complex, a subset is generated via another methyltransferase, METTL16 (Ruszkowska et al 2018;Doxtader et al 2018). In contrast to METTL3/METTL14-dependent m 6 As which are typically found within a 'DRACH' motif and often near stop codons, m 6 A modifications generated by METTL16 do not occur within a defined sequence motif and are more often found in introns and within noncoding RNAs (Ruszkowska et al 2018).…”

“…This writer complex targets RNAs containing a 'DRACH' consensus sequence (where 'D' is any nucleotide but cytosine, 'R' is any purine, and 'H' is any nucleotide but guanine), with the cytosine downstream of the substrate adenine being essential for methylation (Liu et al 2014). The human methyltransferase METTL16 can also generate m 6 A modifications, though these residues do not occur within the same 'DRACH' consensus motif and only a very few substrates are known (Ruszkowska et al 2018;Doxtader et al 2018). While m 6 A modifications have been identified throughout the transcriptome, they are most-often enriched around 3' UTRs and stop codons (Meyer et al 2012;Dominissini et al 2012;Ke et al 2015).…”