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. 2017 Feb 16;65(4):751-760.e4.
doi: 10.1016/j.molcel.2016.12.026. Epub 2017 Jan 26.

ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation

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Free PMC article

ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation

Elayanambi Sundaramoorthy et al. Mol Cell. .
Free PMC article

Abstract

Ribosomes that experience terminal stalls during translation are resolved by ribosome-associated quality control (QC) pathways that oversee mRNA and nascent chain destruction and recycle ribosomal subunits. The proximal factors that sense stalled ribosomes and initiate mammalian ribosome-associated QC events remain undefined. We demonstrate that the ZNF598 ubiquitin ligase and the 40S ribosomal protein RACK1 help to resolve poly(A)-induced stalled ribosomes. They accomplish this by regulating distinct and overlapping regulatory 40S ribosomal ubiquitylation events. ZNF598 primarily mediates regulatory ubiquitylation of RPS10 and RPS20, whereas RACK1 regulates RPS2, RPS3, and RPS20 ubiquitylation. Gain or loss of ZNF598 function or mutations that block RPS10 or RPS20 ubiquitylation result in defective resolution of stalled ribosomes and subsequent readthrough of poly(A)-containing stall sequences. Together, our results indicate that ZNF598, RACK1, and 40S regulatory ubiquitylation plays a pivotal role in mammalian ribosome-associated QC pathways.

Keywords: protein homeostasis; protein modification; ribosome-associated quality control; translation control; ubiquitin.

Figures

Figure 1
Figure 1. Poly(A) Sequence-Induced Translational Repression Is Mediated by ZNF598 and RACK1
(A) Schematic of dual fluorescence translation stall reporters. Plasmids expressing a reporter without a stall-inducing sequence or one containing 20 consecutive lysine codons (AAA, K20) in the linker region were transfected into 293T cells. The resulting cellular GFP and ChFP levels are depicted in the fluorescence-activated cell sorting (FACS) plots. (B) Reporter plasmids containing either no stall sequence (C) or the indicated stall sequence were transfected into 293T cells and analyzed by flow cytometry. The relative ChFP:GFP ratio is depicted for each reporter. K12, 12 lysine codons (AAA); K20, 20 lysine codons (AAA); R2, two arginine codons (CGA); R10, ten arginine codons (CGA); SL, stem loop. (C) 293T cells were transfected with three separate siRNA oligos targeting the indicated genes and subsequently transfected with the K20-containing dual fluorescence reporter. The relative ChFP:GFP ratio is depicted. C, control scrambled siRNA. (D) 293T cells were transfected with control siRNA or siRNA targeting RACK1 or ZNF598 either individually or in combination. The resulting relative ChFP:GFP ratio from the K20 reporter plasmid is depicted. Error bars represent SEM for three separate transfections and flow cytometry measurements. *p < 0.01 using Student’s t test compared with control transfections. See also Figures S1 and S2.
Figure 2
Figure 2. Regulatory Ubiquitylation of RPS20 and RPS10 Is Mediated by ZNF598 and Facilitates Translation Stall Resolution
(A) K20 reporter ChFP:GFP ratios in 293T cells with stable expression of FLAG-HA (FH)-tagged wild-type (WT) RPS20, RPS2, or RPS10 or versions containing the indicated lysine-to-arginine mutations. Error bars represent SEM for three separate transfections and flow cytometry measurements. *p < 0.01 using Student’s t test, comparing cells expressing mutant ribosomal proteins with cells expressing wild-type ribosomal proteins. (B) K20 reporter ChFP:GFP ratios in parental HCT116 cells, ZNF598-KO cells, or ZNF598-KO cells with stable ectopic expression of FLAG-HA-tagged wild-type or C29A mut ZNF598. *p < 0.01 using Student’s t test, comparing parental cells with ZNF598-engineered cell lines. Inset: whole-cell extracts from parental HCT116 cells, ZNF598-KO cells, or ZNF598-KO cells with exogenous FLAG-HA-tagged wild-type or mutant ZNF598 expression were immunoblotted with the indicated antibodies. #, non-specific band. (C) Schematic of SILAC-based proteomic experiments. (D) Scatterplot of the Log2 SILAC ratio (L:H) for all quantified ubiquitin-modified peptides from ZNF598-KO cells and ZNF598-KO cells with exogenous wild-type ZNF598 expression (light) compared with unlabeled (heavy) parental HCT116 cells. Selected ubiquitin-modified peptides from RPS10 are shown in red. (E) Log2 SILAC ratio (L:H) for selected ubiquitin-modified peptides from 40S ribosomal proteins in ZNF598-KO cells (black bars), ZNF598-KO cells with exogenous wild-type ZNF598 expression (red bars), or ZNF598-KO cells with exogenous mutant ZNF598 expression (blue bars) compared with parental cells. The site of ubiquitin modification is indicated. Error bars represent SEM from multiple peptide mass spectrometry (MS) quantifications. (F) Parental HCT116 cells, ZNF598-KO cells, or ZNF598-KO cells rescued with exogenous wild-type or mutant ZNF598 expression were untreated or treated with HTN or DTT for 4 hr. Whole-cell extracts were analyzed by SDS-PAGE and immunoblotted with the indicated antibodies. s and l denote short or long exposures, respectively. See also Figure S3.
Figure 3
Figure 3. Overexpression of ZNF598 Enhances PolyA-Mediated Stall Resolution and RPS10, RPS20, and RPS3 Ubiquitylation in a Ligase-Dependent Manner
(A) K20 reporter ChFP:GFP ratios in parental 293T cells or 293T cells with stable expression of wild-type or mutant ZNF598. *p < 0.01 using Student’s t test compared with parental 293T cells. (B) Parental 293T cells or 293T cells with stable expression of wild-type or mutant ZNF598 were untreated or treated with HTN or DTT for 4 hr. Whole-cell extracts were analyzed by SDS-PAGE and immunoblotted with the indicated antibodies. (C) Native whole-cell lysates from 293T cells with stable expression of wild-type or mutant ZNF598 were separated on a linear 5%–45% sucrose density gradient. The percent relative absorbance at 254 nm is depicted as fractions collected, with vertical gray lines signifying fraction boundaries. 0-mm distance indicates the top of the tube. (D) Fractions from the linear sucrose density gradient from cells overexpressing wild-type (top) or mutant (bottom) ZNF598 were immunoblotted with the indicated antibodies.
Figure 4
Figure 4. Ribosome-Associated RACK1 Facilitates RRub and Translation Stall Resolution
(A) 293T cells were transfected with control siRNA or three separate siRNA oligos targeting RACK1. Cells were then left untreated or treated with HTN or DTT for 4 hr. Whole-cell extracts were analyzed by SDS-PAGE and immunoblotted with the indicated antibodies. Arrows indicate the position of ubiquitylated RP20 or RPS10. (B) Parental 293T cells or cells expressing siRNA-resistant versions (resistant to siRNA #3) of FLAG-HA-tagged wild-type RACK1 or DEmut RACK1 (R36D;K38E) were transfected with control siRNA or two separate RACK1-targeting siRNAs. K20 reporter ChFP:GFP ratios are depicted. Error bars represent SEM from triplicate experiments. *p < 0.01 using Student’s t test, comparing control siRNA transfected cells with RACK1 knockdown cells. The red asterisk denotes the comparison between the parental 293T cell line transfected with si#3 targeting RACK1 and the cell lines expressing si-resistant wild-type or DEmut RACK1 transfected with si#3. NS, not significant. (C) Parental 293T cells or cells expressing siRNA-resistant versions of wild-type RACK1 or DEmut RACK1 were transfected with control siRNA or siRNA#3 targeting the endogenous RACK1 and then left untreated or treated with HTN or DTT for 4 hr. Whole-cell extracts were analyzed by SDS-PAGE and immunoblotted with the indicated antibodies. (D) K20 reporter ChFP:GFP ratios from parental HCT116 cells or two separate ZNF598-KO clones (G,N) transfected with control siRNA or siRNA targeting RACK1 (oligo#3). Error bars represent SEM from triplicate experiments. *p < 0.01 using Student’s t test, comparing control siRNA-transfected cells with RACK1 knockdown cells. See also Figure S4.

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