How Elongator Acetylates tRNA Bases

Abstract

Elp3, the catalytic subunit of the eukaryotic Elongator complex, is a lysine acetyltransferase that acetylates the C5 position of wobble-base uridines (U₃₄) in transfer RNAs (tRNAs). This Elongator-dependent RNA acetylation of anticodon bases affects the ribosomal translation elongation rates and directly links acetyl-CoA metabolism to both protein synthesis rates and the proteome integrity. Of note, several human diseases, including various cancers and neurodegenerative disorders, correlate with the dysregulation of Elongator's tRNA modification activity. In this review, we focus on recent findings regarding the structure of Elp3 and the role of acetyl-CoA during its unique modification reaction.

Keywords: Elongator; Elp3; acetyl-CoA; cancers; neurodegenerative diseases; proteome balance; tRNA modification.

Figure 1

Protein acetyltransferases and Elp3s structures. (a) Structures of KAT domain from TtGcn5 (PDB: 1QSN), HsMYST (PDB: 2PQ8), and Hsp300 (PDB: 5LKT) and the GNAT domain from HsNaa50 (PDB: 6PPL). (b) Elp3 structures from D. mccartyi (PDB: 5L7J), M. infernus (PDB: 6IAD), and S. cerevisiae (PDB: 6QK7). Domains of each enzyme are as indicated.

Figure 2

Biochemical features of Elp3. (a) Illustrations of the Elp3-dependent cm⁵U modification reaction (left) and the crystal structure of the acetyl-CoA binding pocket of DmcElp3 with desulfo-CoA (right, PDB: 6IA6). The components in the cm⁵U reaction are as indicated. The ligand contacting residues are labeled, while the conserved lysine (Lys77 in DmcElp3) is highlighted in red. (b) Schemes of the proposed tRNA-triggered acetyl-CoA hydrolysis of Elp3 (left) and Gcn5-mediated protein acetylation mechanism (right). The modifiable U₃₄ and reactive K₁₄ of histone H3 peptide are colored in red. For a clearer presentation, the α1 and α2 helices of TtGcn5 are shown in a transparent style. Acetyl-CoA, shown in cartoon, is modeled in the binding pockets of Elp3 or Gcn5, whereas the chemical structure of acetyl-CoA is shown on the top and the reactive carbons are highlighted in an orange circle (acetyl radical for cm⁵ modification) or purple circle (carbonyl group of the thioester of acetyl-CoA). The reactive sites of cm⁵U₃₄ and Ac-Lys are both colored in red and present the C-C bond for the cm⁵ addition and the C-N bond for the acetyl-lysine addition, respectively.

Figure 3

Elongator-mediated tRNA modification and clinically relevant mutations of human Elp3. (a) Schemes of disease-related mutations and Elongator-mediated tRNA modification cascade. The reported changes in human Elp3 from neurodegenerative diseases (ND) are indicated, while those of tumors (data were retrieved from COSMIC, ICGC, and TCGA databases) are shown in the Venn diagram. tRNA (black) binds to one lobe of Elp123 that is involved in Elp456 dynamic interactions. Elp3 hydrolyzes acetyl-CoA and cleaves SAM for the cm⁵ addition on U₃₄. The cm⁵U₃₄ is then converted to the derivatives by other enzymes. (b) Summary of reported alterations and PTM sites of mouse Elp3 (p-Ser161) and human Elp3 (p-Tyr202 and m-Lys229). The residue numbers and domains of human Elp3 are indicated. The locations of the alterations are as listed in the cartoon representation and they are color-coded according to which database resources are found. The experimentally verified residues are indicated with an asterisk. The identified PTM sites (solid circles) of Elp3 as well as the catalytic residues for acetyl-CoA binding/hydrolysis (open square) in Elp3 are listed.