Diversity and Similarity of Termination and Ribosome Rescue in Bacterial, Mitochondrial, and Cytoplasmic Translation

Abstract

When a ribosome encounters the stop codon of an mRNA, it terminates translation, releases the newly made protein, and is recycled to initiate translation on a new mRNA. Termination is a highly dynamic process in which release factors (RF1 and RF2 in bacteria; eRF1•eRF3•GTP in eukaryotes) coordinate peptide release with large-scale molecular rearrangements of the ribosome. Ribosomes stalled on aberrant mRNAs are rescued and recycled by diverse bacterial, mitochondrial, or cytoplasmic quality control mechanisms. These are catalyzed by rescue factors with peptidyl-tRNA hydrolase activity (bacterial ArfA•RF2 and ArfB, mitochondrial ICT1 and mtRF-R, and cytoplasmic Vms1), that are distinct from each other and from release factors. Nevertheless, recent structural studies demonstrate a remarkable similarity between translation termination and ribosome rescue mechanisms. This review describes how these pathways rely on inherent ribosome dynamics, emphasizing the active role of the ribosome in all translation steps.

Keywords: rescue; ribosome; termination; translation.

Fig. 1.

Bacterial translation termination involves large-scale conformational changes, a-d) Cryo-EM structures demonstrating rearrangements of a release factor and intersubunit rotation of a bacterial 70S ribosome upon stop-codon recognition and peptide release. E. coli RF2 is shown: panels (b and c) [51 ]and d [61], The decoding center (DC) and peptidyl transferase center (PTC) are labeled in panel (a). Crystal structure of free RF2 is shown between panels (a) and (b) [40], Domain organization for RF1/RF2 is shown with Arabic numerals in panel (c). e) Cryo-EM structure of RF1 and RF3 on E. coli ribosome with P/E tRNA and rotated 30S subunit [58], f) Cryo-EM structure of the pre-recycling E. coli ribosome with P/E tRNA and rotated 30S subunit after dissociation of release factors [61], g and h) Rearrangement of the codon and decoding center (DC) upon binding of RF2 (Structure II in [61]). Stop codon and DC in panel g were modeled based on Structure I in ref. [54], i) Rearrangement of RF2 in the peptidyl transferase center (PTC; [61]). The catalytic conformation of RF2 with the GGQ-bearing α-helix is shown in pink and the ribosome is shown in gray. The β-hairpin conformation of RF2 (red) coincides with movement of A2602 and departure of tRNA (orange) from the PTC (cyan).

Fig. 2.

Ribosome rescue and release mechanisms involving bacterial factors ArfA and ArfB, and mitochondrial factors mtRF1a, ICT1 and mtRF-R. a and b) Cryo-EM structures of E. coli ribosomes with truncated mRNA, ArfA and compact (a) or extended (b) RF2 [49]. c) A close-up view of interactions between ArfA, RF2, mRNA and P-site tRNA. d-g) Cryo-EM structures of E. coli ribosomes with truncated mRNA (with a 0- or 9-nt-long overhang after the P site codon) and ArfB [110, 111], h) Cryo-EM structure of porcine mitochondrial 55S termination complex with mtRF1a bound to the stop codon [87] closely resembles bacterial termination complexes with RF1. i) Cryo-EM structure of mitochondrial 55S rescue complex with ICT1 [87] closely resembles bacterial 70S complex with ArfB [compare to panel (e)]. j) Cryo-EM structure of large mitochondrial subunit bound with human rescue factor mtRF-R and auxiliary factor MTRES1 [98].

Fig. 3.

Eukaryotic translation termination and cytoplasmic ribosome rescue mechanisms, a-c) Rearrangements of release factor eRF1 on the 80S ribosome with a stop codon upon GTP hydrolysis on eRF3 (a-b) and interaction with recycling factor ABCE1 (c; Rli1 in yeast), d) Interaction of the catalytic conformation of eRF1 with the P-site tRNA [137], e) Recognition of the 4-nucleotide stop signal by eRF1 involves residues of the TASNIKS motif (Ile62 and Fys63 are shown) and G626 of 18S rRNA [137], f and g) Rearrangements of Pelota (Dom34 in yeast) on the 80S ribosome with truncated mRNA upon GTP hydrolysis on Hbs1 [163] and binding of ABCE1 [164], h) Recognition of truncated mRNA by Dom34 [163], i) Interaction of the extended conformation of Dom34 with the P-site tRNA [164], j) 60S rescue complex with peptidyl-tRNA hydrolase Vms1 and Arb1 [165], k) Interaction of Vms1 and Arb1 with the tRNA.