Trm112, a Protein Activator of Methyltransferases Modifying Actors of the Eukaryotic Translational Apparatus

Abstract

Post-transcriptional and post-translational modifications are very important for the control and optimal efficiency of messenger RNA (mRNA) translation. Among these, methylation is the most widespread modification, as it is found in all domains of life. These methyl groups can be grafted either on nucleic acids (transfer RNA (tRNA), ribosomal RNA (rRNA), mRNA, etc.) or on protein translation factors. This review focuses on Trm112, a small protein interacting with and activating at least four different eukaryotic methyltransferase (MTase) enzymes modifying factors involved in translation. The Trm112-Trm9 and Trm112-Trm11 complexes modify tRNAs, while the Trm112-Mtq2 complex targets translation termination factor eRF1, which is a tRNA mimic. The last complex formed between Trm112 and Bud23 proteins modifies 18S rRNA and participates in the 40S biogenesis pathway. In this review, we present the functions of these eukaryotic Trm112-MTase complexes, the molecular bases responsible for complex formation and substrate recognition, as well as their implications in human diseases. Moreover, as Trm112 orthologs are found in bacterial and archaeal genomes, the conservation of this Trm112 network beyond eukaryotic organisms is also discussed.

Keywords: RNA modifying enzyme; S-adenosyl-l-methionine; methyltransferase; post-transcriptional modification; translation.

Figure 1

Organization of eukaryotic Trm112 proteins. (a) Ribbon representation of the crystal structure of isolated Saccharomyces cerevisiae Trm112 protein with a schematic representation of eukaryotic Trm112 shown below with the domain’s color code. (b) Sequence alignment of eukaryotic Trm112 protein sequences. Amino acids forming the Zn-knuckle and helical domains are identified by pink and blue bars, respectively, above the sequences. The positions of the four cysteine residues coordinating the zinc atom in the structures of fungal and Encephalitozoon cuniculi Trm112 proteins are indicated by black spheres below the alignment. Secondary structure elements as observed in the structure of the S. cerevisiae Bud23-Trm112 complex are indicated above the sequences [20]. Sequences have been divided into two subgroups: fungal proteins (Subgroup 1) and metazoans (Subgroup 2). Strictly-conserved residues are in white on a red background. Strongly-conserved residues are in red. This figure was generated using the Espript server [22]. C-ter: C-terminal protein extremity; N-ter: N-terminal protein extremity.

Figure 2

Schematic representation of the Trm112- methyltransferase (MTase) interaction network and of the substrates of these complexes. The surface representation of the aRF1-aRF3 complex from Aeropyrum pernix archeon was generated using PDB Code 3VMF [25]. Positions 10, 26 and 34 on a tRNA molecule are shown in purple, grey and green, respectively. The position of G₁₅₇₅ on 18S rRNA is shown as a beige sphere. The color code used to depict the various partners will be used in all figures of this review.

Figure 3

Crystal structure of the Yarrowia lipolytica (Yl) Trm9-Trm112 complex. (a) Ribbon representation of the YlTrm9-Trm112 complex. The S-adenosyl-l-methionine (SAM) molecule (grey sticks), which was absent in the crystal structure, has been modeled by superimposing the SAM-bound structure of Bud23 onto YlTrm9. The Trm9 lid is colored yellow. (b) Model of cm⁵U₃₄ (blue sticks) docked into the YlTrm9 active site. The SAM methyl group to be transferred is depicted as a sphere. Residues are numbered according to the S. cerevisiae protein.

Figure 4

Ribbon representation of the crystal structure of the Encephalitozoon cuniculi (Ecu) Mtq2-Trm112 complex bound to SAM (grey sticks).

Figure 5

Crystal structure of the S. cerevisiae (Sc) Bud23-Trm112 complex. (a) Ribbon representation of the ScBud23-Trm112 complex bound to SAM. (b) Model of guanosine monophosphate (GMP) (blue sticks) bound to the ScBud23 active site.

Figure 6

Comparison of the Trm112-MTase interfaces. (a) Ribbon representation of the β-zipper interaction between Trm112 and MTases. Hydrogen bonds formed between main chain atoms from both partners are depicted by grey dashed lines. (b) Comparison of ScBud23-Trm112 and YlTrm9-Trm112 structures reveals conserved hotspots involved in complex formation. A structure-based sequence alignment of YlTrm9 and of the four S. cerevisiae MTases interacting with Trm112 is shown in the lower panel. Only a small region of these MTases is shown for the sake of clarity.

Figure 7

Trm112 is present in the three domains of life. (a) Simplified phylogenetic tree of Trm112. Emphasis is given to archaeal phylogeny. The distribution of Trm11, Trm9, Mtq2 and Bud23 proteins within the three domains of life is indicated. The various Trm112 forms identified are schematically depicted. (b) Ribbon representation of Streptomyces coelicolor SCO3027 protein nuclear magnetic resonance (NMR) structure (PDB Code 2KPI). Cysteine residues coordinating the zinc atom (grey sphere) bound to the protein are shown as sticks. (c) Superimposition of Streptomyces coelicolor SCO3027 structure (pink) onto Trm112 in the ScBud23-Trm112 complex (Trm112 and Bud23 are colored red and beige, respectively). The SAM molecule bound to Bud23 is shown as grey sticks.