Structural and functional insights into Archaeoglobus fulgidus m2G10 tRNA methyltransferase Trm11 and its Trm112 activator

Abstract

tRNAs play a central role during the translation process and are heavily post-transcriptionally modified to ensure optimal and faithful mRNA decoding. These epitranscriptomics marks are added by largely conserved proteins and defects in the function of some of these enzymes are responsible for neurodevelopmental disorders and cancers. Here, we focus on the Trm11 enzyme, which forms N2-methylguanosine (m2G) at position 10 of several tRNAs in both archaea and eukaryotes. While eukaryotic Trm11 enzyme is only active as a complex with Trm112, an allosteric activator of methyltransferases modifying factors (RNAs and proteins) involved in mRNA translation, former studies have shown that some archaeal Trm11 proteins are active on their own. As these studies were performed on Trm11 enzymes originating from archaeal organisms lacking TRM112 gene, we have characterized Trm11 (AfTrm11) from the Archaeoglobus fulgidus archaeon, which genome encodes for a Trm112 protein (AfTrm112). We show that AfTrm11 interacts directly with AfTrm112 similarly to eukaryotic enzymes and that although AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. We finally describe the first crystal structures of the AfTrm11-Trm112 complex and of Trm11, alone or bound to the methyltransferase inhibitor sinefungin.

Human mitochondrial protein complexes revealed by large-scale coevolution analysis and deep learning-based structure modeling

“…Interestingly, Trm112 proteins are subunits of multifunctional methyltransferases that form complexes with and activate the tRNA methyltransferases such as Trm11 and Trm9. Structures of the recently solved archaeal Trm112-Trm11 complexes [86, 87] revealed similar interaction sites as predicted by AlphaFold2 in PYURF and NDUFAF5. Our coevolution analysis as well as the remote homology of PYURF to Trm112 proteins suggests that PYURF is a subunit that forms a complex with the NDUFAF5 hydroxylase and could play an essential role in the catalytic activity.…”

Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases?

“…Reciprocally, SAM binding seems to strengthen the interaction between TRMT112 and some MTases as shown for Trm9 or Mtq2 mutants unable to interact with SAM and that co-purify less efficiently with Trm112 in yeast (Lacoux et al, 2020;Liger et al, 2011). Finally, a conserved region from TRMT112 that comes into close proximity from the MTase active sites, contributes to substrate binding by at least yeast Mtq2 and Trm11 enzymes but not BUD23 according to the cryo-EM of the human BUD23-TRMT112 complex bound to a late 40S (Ameismeier, Cheng, Berninghausen & Beckmann, 2018;Liger et al, 2011;Wang et al, 2020).…”

“…First, the crystal structures of most TRMT112-MTase complexes have been solved (Fig. 6B-F), revealing that although these various MTases from the same or-ganism share less than 25%, they all compete to interact in a very similar way with TRMT112 (Bourgeois, Letoquart, van Tran & Graille, 2017;Letoquart et al, 2014;Letoquart et al, 2015;Liger et al, 2011;Metzger et al, 2019;van Tran et al, 2019;Wang et al, 2020). Indeed, the same region from their MTase domains, i.e.…”

“…Most of the pioneer studies on TRMT112 network where performed using S. cerevisiae as model organism and then replicated in human cells, demonstrating the strong conservation of the function of these enzymes across evolution. Recently, the TRMT112 interaction network has been characterized in archaea, revealing that the biochemical activities of four eukaryotic TRMT112-MTase complexes are conserved in archaea, thereby emphasizing on the strong similarities between eukaryotic and archaeal translation machineries (van Tran et al, 2019;van Tran et al, 2018;Wang et al, 2020).…”

Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine-N2-) Methyltransferase (Trm11-Trm112 Complex)

“…Trm11 works as a catalytic subunit while Trm112 is a regulatory subunit [ 4 , 5 , 6 , 7 ]. Although the crystal structure of the Trm11-Trm112 complex from S. cerevisiae has not been reported, a structural model has been proposed based on the structures of archaeal orthologs and a combination of biochemical, biophysical and bioinformatic studies [ 8 , 9 , 10 ]. Trm11 is a typical Rossmann fold S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase (COG 1041) with a thiouridine synthase, methyltransferase and pseudouridine synthase (THUMP) domain fused to its N-terminal region [ 4 , 5 , 8 , 9 , 10 ].…”