Mitoribosome Biogenesis

Abstract

Mitoribosome biogenesis is a complex and energetically costly process that involves RNA elements encoded in the mitochondrial genome and mitoribosomal proteins most frequently encoded in the nuclear genome. The process is catalyzed by extra-ribosomal proteins, nucleus-encoded assembly factors that act in all stages of the assembly process to coordinate the processing and maturation of ribosomal RNAs with the hierarchical association of ribosomal proteins. Biochemical studies and recent cryo-EM structures of mammalian mitoribosomes have provided hints regarding their assembly. In this general concept chapter, we will briefly describe the current knowledge, mainly regarding the mammalian mitoribosome biogenesis pathway and factors involved, and will emphasize the biological sources and approaches that have been applied to advance the field.

Keywords: Mitochondrial disease; Mitochondrial ribosome; Mitochondrial translation; Mitoribosome assembly; OXPHOS deficiency.

Figure 1.. The human mitochondrial ribosome.

High-resolution 2.2 Å consensus map of the human mitoribosome viewed from the beak side (A) and platform side (B) highlighting mitochondrial-specific proteins in red. The mtSSU 12S rRNA is displayed in light purple and proteins conserved in bacteria are shaded dark purple. In the mtLSU the 16S rRNA is colored light blue, the CP-tRNA in cyan, and bacterial-like proteins in sea green. Solvent and intersubunit views of the mtSSU (C) and mtLSU (D) with proteins shown as cartoons using the atomic model and RNA components as density maps. The path of mRNA during translation is indicated in yellow and the polypeptide exit tunnel in white. Atomic model of mitoribosome proteins individually annotated and colored (E). RNA components are shown as density maps and colored as in panels A-D. Bound nucleotides ATP and GDP are labeled in red, iron-sulfur clusters in yellow, and the mRNA in pink. EM map used is EMD-13980 and atomic coordinates are PDB-7QI4.

Figure 2.. Features of tRNA binding in the human mitoribosome.

(A) Cryo-EM map of the human mitoribosome highlighting RNA elements. The mtSSU and mtLSU rRNAs are shown in dark purple and sea green, respectively, while the tRNAs are indicated in cyan (CP-tRNA), light green (A-site tRNA), yellow (P-site tRNA), and orange (E-site tRNA). Mitoribosomal proteins are transparent and shown as a surface outline. (B) Depiction of proteins involved in tRNA binding, stabilization, and movement during translation. Individual proteins are colored and labeled. Proteins are shown using atomic coordinates with helices as tubes and RNA elements as cartoons with bases as ladders. (C-D) Zoomed-in-view of protein-RNA interactions. Nearby structural elements were removed for clarity. EM map is EMD-11397 and atomic coordinates are PDB-6ZSG.

Figure 3.. Mitoribosome SSU assembly.

Model of human 28S mtLSU biogenesis depicting a hierarchical and module-based protein assembly pathway, including known assembly factors at their approximate stage of incorporation. All modules are color-coded. The assembly process is divided in three stages: early (red arrows), intermediate (green arrows) late (blue arrows) (see explanation in the text) Boxes, highlighted with the same color used in the spiral assembly, represent different protein clusters at different assembly stages.

Figure 4.. Mitoribosome LSU assembly.

Model of human 39S mtLSU assembly pathway, including known assembly factors at their approximate stage of incorporation. All modules are color-coded. Boxes represent different protein clusters at different assembly stages: early (red arrows), intermediate (green arrows) late (blue arrows) (see explanation in the text).