Structure of mitoribosome reveals mechanism of mRNA binding, tRNA interactions with L1 stalk, roles of cofactors and rRNA modifications

Abstract

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 A resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transition in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide the most complete description so far of the structure and function of the human mitoribosome.

Structural Basis of T Cell Toxicity Induced by Tigecycline Binding to the Mitochondrial Ribosome

“…These conformational changes are accompanied by a downward shift of helix 71 (~ 4-5 Å) as compared to the untreated monosome (Fig. 4B) 32 . Additionally, nucleotide C2603 ips inward together with A2600, with which it forms stacking interactions (Fig.…”

“…Tigecycline occupies the PTC, with its 9-t-butylglycylamido substituent stretching adjacent to the P-tRNA (green), and the A ring interacting with the mL45 N-terminal extension (pink). Upon tigecycline binding, A2725 nucleobase shifts and stacks against ring D in both the P-tRNA only and the A-(blue), P-tRNA mitoribosomal classes, as compared to the untreated (tigecycline) mitoribosome (PDB:7QI4 32 ). G2992, U2993, and G3063 in the PTC rearranges upon binding of the A-tRNA (as also observed for the untreated mitoribosomes).…”

The catalytic activity of methyltransferase METTL15 is dispensable for its role in mitochondrial ribosome biogenesis

“…In humans, mitochondrial translation sometimes starts with AUA or AUU instead of AUG. Recent structural study focusing on the mt-rRNA modifications within the mitoribosome, demonstrated that the m 4 C1486 interacts with the phosphate group of the last nucleotide in the P-site mRNA codon via hydrogen bonding [ 30 ]. Speculatively, m 4 C1486 methylation may refine the P-site’s structure, impacting on decoding accuracy for these codons, but its importance needs further investigation.…”

Molecular Investigation of Mitochondrial RNA19 Role in the Pathogenesis of MELAS Disease

“…In support of this, RNA19 has been shown to bind PTCD1, a protein required for 16S mt-rRNA maturation and ribosome assembly [ 32 ]. Indeed, from the inspection of the most recent 3D structure of the human mitoribosome at 2.2 Å resolution [ 33 ], the hypothetical ‘tail’ of RNA19 (consisting of mt-tRNALeu UUR and mt-ND1 mRNA) would protrude from the surface of the mt-LSU in close proximity to uL3m, bL17m and mL39 ( Figure S5 ). The latter, together with mL45, is part of a protein layer that surrounds the polypeptide exit site; it shows homology with RNA-binding proteins whose regions for RNA binding are oriented towards the solvent and not used for interaction with rRNA [ 34 ].…”