Quality control ensures fidelity in ribosome assembly and cellular health

Abstract

The coordinated integration of ribosomal RNA and protein into two functional ribosomal subunits is safeguarded by quality control checkpoints that ensure ribosomes are correctly assembled and functional before they engage in translation. Quality control is critical in maintaining the integrity of ribosomes and necessary to support healthy cell growth and prevent diseases associated with mistakes in ribosome assembly. Its importance is demonstrated by the finding that bypassing quality control leads to misassembled, malfunctioning ribosomes with altered translation fidelity, which change gene expression and disrupt protein homeostasis. In this review, we outline our understanding of quality control within ribosome synthesis and how failure to enforce quality control contributes to human disease. We first provide a definition of quality control to guide our investigation, briefly present the main assembly steps, and then examine stages of assembly that test ribosome function, establish a pass-fail system to evaluate these functions, and contribute to altered ribosome performance when bypassed, and are thus considered "quality control."

Figure 1.

Cartoon overview of SSU processome and nuclear pre-40S assembly. (A) Schematic of the pre-rRNA encoding 18S, 5.8S, and 25S rRNAs. (B) Numbers 1–2 represent two potential QC steps: (1) balancing 40S:60S subunit production and (2) maturation of the ribosome neck. Described in more detail in the section titled “Nucleolar and nuclear pre-40S assembly.”

Figure 2.

Cartoon of cytoplasmic pre-40S assembly. Numbers 1–3 represent three QC steps: (1) testing scanning and translation initiation, (2) evaluation of translocation, and (3) inspection of 18S rRNA cleavage. Described in more detail in the section titled “Cytoplasmic pre-40S assembly overview.”

Figure 3.

Schematic of QC step testing scanning competence of pre-40S ribosome. (A) QC mechanisms check for proper incorporation of RPs and folding of 18S rRNA in the ribosomal head before forming the scanning competent 80S-like ribosome. Failure to pass QC results in turnover of these pre-40S intermediates. (B) On the other hand, bypass of QC by using a weakly binding Enp1 mutant (yellow star) allows pre-40S with misfolded rRNA and mispositioned RPs to form 80S-like ribosomes that are eventually released into the translating pool, where they will have defects in start codon selection (Huang et al., 2020). (C) Structure of the human pre-40S ribosomal subunit (gray) bound by BYSL (yellow), LTV1 (orange), and RIOK2 (red; PDB accession no. 6G18; Ameismeier et al., 2018). Colored spheres indicate residues in BYSL (Enp1) that are mutated in cancer and are predicted to bypass QC (dark blue spheres indicate point mutations in residues R303 and P318, while cyan spheres mark nonsense mutations at Y265 and R267 that produce truncated Enp1 protein). Inset on the left has RPs removed for clarity (TCGA www.cancer.gov/tcga, cBioPortal www.cbioportal.org).

Figure 4.

Schematic of Fap7-mediated QC step verifying translocation capability of the pre-40S subunit. (A) Fap7 releases Dim1 to allow pre-40S to continue their assembly only after confirming that the pre-40S can form the rotated state needed to maintain the reading frame during translation. Failure to pass this QC results in turnover of 80S-like intermediates. (B) Bypass of this QC using a weakly binding Dim1 mutant (yellow star) allows 40S subunits to continue maturation and causes −1 frameshifting during translation (Ghalei et al., 2017). (C) Structure of the 80S-like ribosome (gray, 60S is omitted for clarity) bound by Dim1 (yellow) and Tsr1 (blue; PDB accession no. 6WDR; Rai et al., 2021). Dim1_EKR (E93/K96/R97) is shown in red spheres. Dark blue spheres indicate residues in DIMT1 (P88A, P88T, D113N, N219T, and R228M) that are mutated in cancer and are predicted to bypass QC (TCGA www.cancer.gov/tcga, cBioPortal www.cbioportal.org).

Figure 5.

Schematic of Rio1-mediated QC step monitoring 18S rRNA cleavage. (A) QC mechanism regulated by Rio1 ensures only ribosomes with precise 18S rRNA cleavage are licensed to translate. The red loop on the ribosomes next to Nob1 indicates ITS1 in pre-18S rRNA. Failure to pass this QC step results in turnover of these 80S-like intermediates. (B) Bypassing QC via weakly binding Pno1 mutations leads to the release of ribosomes containing uncleaved 20S pre-rRNA or miscleaved 18S rRNA into the translating pool, where they cause errors in translation (20S pre-rRNA–containing ribosomes; Parker et al., 2019) or ribosome collisions (miscleaved 18S rRNA-containing ribosomes—not shown; Parker et al., 2022 Preprint). (C) Structure of the human pre-40S ribosomal subunit (3′-end of 18S rRNA is gray and RPs are removed for clarity) bound by PNO1 (purple) and NOB1 (green and black; PDB accession no. 6ZXE; Ameismeier et al., 2020). Colored spheres indicate residues in PNO1 or NOB1 that are mutated in cancer and are predicted to bypass QC. Pink spheres indicate nonsense mutations in NOB1 (C234, Y334, and Q348) and black indicates the section of NOB1 truncated after S325 (homologous to yeast Nob1_1-363; Parker et al., 2019). Mutations in PNO1 include PNO1_K186/K189/K191/F192 (homolog to yeast Pno1_KKK/F; yellow) and cancer mutations PNO1_T190N (homolog to yeast Pno1_T212N; cyan) and PNO1_R84I, P87Q, A184T (orange; TCGA www.cancer.gov/tcga, cBioPortal www.cbioportal.org).

Figure 6.

Cartoon of pre-60S assembly. Numbers 1–3 represent three potential QC steps: (1) inspecting A-site methylation, (2) testing PTC assembly, and (3) testing translational GTPase activation. Described in more detail in the section titled “Overview of pre-60S assembly.” The 5S RNP (consisting of the 5S rRNA, Rpl5, and Rpl11) is green and 25S:G_m2922 methylation is represented by a red star. SAM: S-adenosyl-methionine; SAH: S-adenosyl-homocysteine.