Structure and assembly pathway of the ribosome quality control complex

Abstract

During ribosome-associated quality control, stalled ribosomes are split into subunits and the 60S-housed nascent polypeptides are poly-ubiquitinated by Listerin. How this low-abundance ubiquitin ligase targets rare stall-generated 60S among numerous empty 60S is unknown. Here, we show that Listerin specificity for nascent chain-60S complexes depends on nuclear export mediator factor (NEMF). The 3.6 Å cryo-EM structure of a nascent chain-containing 60S-Listerin-NEMF complex revealed that NEMF makes multiple simultaneous contacts with 60S and peptidyl-tRNA to sense nascent chain occupancy. Structural and mutational analyses showed that ribosome-bound NEMF recruits and stabilizes Listerin's N-terminal domain, while Listerin's C-terminal RWD domain directly contacts the ribosome to position the adjacent ligase domain near the nascent polypeptide exit tunnel. Thus, highly specific nascent chain targeting by Listerin is imparted by the avidity gained from a multivalent network of context-specific individually weak interactions, highlighting a new principle of client recognition during protein quality control.

Graphical abstract

Figure 1

NEMF Is Required for Listerin Recruitment to Stalled Ribosomes (A) HEK293T cells treated for 30 min with DMSO (control), 50 μg/ml CHX, or 1 mM puromycin (puro) were lysed and the cytosolic extracts separated on 10%–50% sucrose gradients. Eleven fractions from top (fraction 1) to bottom (fraction 11) were analyzed for the distribution of Listerin. The immunoblots and their respective quantification are shown. (B) The A₂₆₀ profiles of the sucrose gradients from (A) are shown. As shown in Figure S1A, fractions 5 corresponds to 60S, fraction 6 to 80S, and fractions 7–11 to polysomes. (C) Immunoblotting of the samples from (A) for NEMF recruitment to ribosomes. (D) Cytosolic extract from CHX-treated cells as in (A) were size fractionated on a high-resolution 10%–30% sucrose gradient and immunoblotted for the indicated components. The positions of 60S and 80S are indicated. L9 (uL6) and S16 (uS9) are small and large subunit proteins, respectively. T indicates total lysate. Asterisk indicates background band. The plus symbol indicates multiple fractions were pooled (e.g., 5+ is fractions 5–8). (E) HEK293T cells transfected for 30 hr with mock or NEMF siRNAs were analyzed for Listerin recruitment to ribosomes as in (A). The inset shows Listerin and NEMF levels in the total cytosol extract. Knockdown of NEMF was to ∼25% of control levels. See also Figure S1.

Figure 2

NEMF Is Sufficient to Stabilize Listerin on 60S RQC Complexes (A) Purified NEMF was titrated into ubiquitination reactions containing 5 nM affinity-purified ³⁵S-labeled stalled 80S-RNCs and 1.2 nM Listerin. All reactions contained splitting factors (50 nM Hbs1, 50 nM Pelota, and 50 nM ABCE1), ubiquitination reagents (75 nM E1, 250 nM UbcH5, and 10 μM ubiquitin), and an energy regeneration system. Reactions were incubated at 32°C for 10 min before analysis by SDS-PAGE and autoradiography. The amount of poly-ubiquitination was quantified and normalized to that seen without NEMF (set arbitrarily to 1). (B) Radiolabeled 80S-RNCs were subjected to ubiquitination reactions containing or lacking NEMF and Listerin as indicated. Reactions were at 32°C for 3 min. Reaction products were analyzed by SDS-PAGE and autoradiography. The tRNA-attached nascent chain (NC-tRNA) and its poly-ubiquitinated species (poly-Ub) are indicated. A parallel aliquot of the reaction was separated by centrifugation to isolate ribosomes. Listerin was detected by immunoblot in the total (middle panel) and ribosome fraction (bottom panel). Asterisk indicates position of a background band. (C) Reactions as in (B) were separated on 10%–30% sucrose gradients and the indicated fractions analyzed by SDS-PAGE and immunoblotting for NEMF or Listerin. The fractions corresponding to 60S and 80S are indicated. (D) 80S-RNCs were incubated with splitting factors and energy without (gray) or with (black) 50 nM NEMF and separated on 10%–30% sucrose gradients. The profiles of the NC-tRNA are displayed. Note that Listerin was not included in these reactions so that NC-tRNA could be visualized as a single band. (E) Ubiquitination reaction of radiolabeled 80S-RNCs with 1.2 nM Listerin and 1.2 nM NEMF were separated on a 10%–30% sucrose gradient and analyzed by autoradiography. Unmodified NC-tRNA, its poly-ubiquitinated species, and the positions of 60S and 80S are indicated. Note that essentially all 60S-RNCs are poly-ubiquitinated, while 80S-RNCs remain largely, if not completely, unmodified. See also Figure S2.

Figure 3

Architecture of 60S-RNCs Bound to NEMF and Listerin (A) Back view of a cryo-EM reconstruction of the 60S-RNC complex showing the ribosome in gray, Listerin in orange, NEMF in teal, and the P-site peptidyl-tRNA in purple. The nascent polypeptide exit tunnel and the ribosomal L1 stalk are indicated for orientation. The map is low-pass filtered to 5 Å and displayed at a threshold to visualize continuous density of the factors. (B) View from the subunit interface of the 60S-RNC complex. The central protuberance (CP) and L1 stalk are shown for orientation. The P stalk of the ribosome is in dark gray. The N-terminal lobe (N), C-terminal lobe (C), and Middle domain (M) of NEMF are labeled. (C) Cut-away view of the 60S-RNC complex showing that the N- and C-lobes of NEMF contact the tRNA and a region of Listerin poised at the exit tunnel. (D) Example of the fit of a docked tRNA (purple), showing the 3′ CCA end, and the de novo model of the defined nascent chain (green) into the EM map density. See also Figure S3.

Figure 4

Structural Features of Listerin Bound to the 60S-RNC (A) View of the exit tunnel side of the 60S ribosomal subunit depicting EM density filtered to 5 Å at a threshold that displays secondary structure. The density for Listerin is orange and fit with structural models of HEAT repeats, the RWD domain, and the RING domain. Models for the following ribosomal protein are also fit in position: eL22 (dark blue), eL31 (light blue), uL23 (gray), and uL29 (gray). The exit tunnel is shown as a dashed circle. (B) Atomic model of Listerin’s RWD domain with the neighboring ribosomal proteins eL22 (dark blue) and eL31 (light blue), depicting possible sites of interaction (arrows). See also Figure S4.

Figure 5

Structural Analysis of NEMF Interactions on the 60S-RNC (A) Side view of the N terminus of Listerin (orange) contacting NEMF (teal) and the 60S subunit (gray) with density for the P stalk in dark gray. De novo models of NEMF’s M-domain and Listerin’s N-terminal helix, along with a poly-alanine model of the helices of Listerin’s N-terminal HEAT repeats is superimposed into the density (filtered at 5 Å). (B) Atomic models of the middle domain of NEMF (NEMF-M, teal), the N-terminal helix of Listerin (orange), eL40 (light blue), uL11 (dark blue), and interacting portions of the 28S rRNA (dark gray). (C) De novo built models of the NEMF-M domain and Listerin's N-terminal helix fit to map density, illustrating a likely interaction. (D) Models fitted to map density illustrating a stacking interaction of W375 of the NEMF-M domain with A4605 of H95/sarcin-ricin loop of the 28S rRNA. (E) View of the M-domain of NEMF (teal) with corresponding positions of the P stalk proteins uL11 (dark blue) and uL10 (light blue) in the map of the 60S subunit in complex with NEMF and Listerin (blue) or of the same proteins in a map of an 80S ribosome bound to eEF2 (gray). See also Figure S5 and Figure S6.

Figure 6

Biochemical Analysis of RQC Assembly and Function (A) Affinity-purified 80S-RNCs were left untreated (black) or incubated with splitting factors in the presence of either NEMF (teal) or eIF6 (purple). Puromycin was then added, the reaction was analyzed by SDS-PAGE at the indicated time points, and the amount of nascent chain released from tRNA by puromycin quantified. (B) Affinity-purified 80S-RNCs were prepared containing a short nascent chain without (F-β tRNA, black) or with (F-V-β tRNA, gray) a small folded domain outside the ribosomal exit tunnel. The RNCs were incubated with 1.2 nM NEMF, 50 nM splitting factors, and energy and analyzed for NEMF recruitment to ribosomes via a 10%–50% sucrose gradient. Upon ribosome splitting, F-β tRNA will “drop out” of the 60S subunit (with ∼50% efficiency), while F-V-β tRNA remains quantitatively trapped. NEMF recruitment to the RNCs is reduced for the drop-off substrate. (C) 80S-RNCs were subjected to ubiquitination reactions with 1.2 nM Listerin, splitting factors, ubiquitination reagents, and energy in the presence of various amounts of free tRNA. One set of reactions contained 1.2 nM NEMF (teal), while the other contained 250 nM eIF6 (purple) to prevent 40S reassociation. Samples were analyzed by SDS-PAGE, autoradiography, and phosphorimaging. The relative amount of poly-ubiquitination compared to the sample without added tRNA was quantified from three independent experiments. Data points represent the mean ± SEM. (D) 80S-RNCs were subjected to ubiquitination reactions with ubiquitination reagents, energy, splitting factors, either 50 nM eIF6 (top) or 1.2 nM NEMF (bottom), and either 1.2 nM wild-type Listerin or increasing amounts of the KR-DD mutant Listerin predicted to abolish the interaction between the RWD domain and eL31 (see Figures 4B and S5D). Reactions with NEMF were for 2 min, while reactions with eIF6 were for 5 min. Autoradiography depicting the nascent chain-tRNA (NC-tRNA) and poly-ubiquitinated species (poly-Ub), and Coomassie staining showing the relative amounts of purified Listerin are shown. (E) Autoradiography of 5 min ubiquitination reactions containing 80S-RNCs, ubiquitination reagents, energy, splitting factors, either 1.2 nM NEMF (top) or 50 nM eIF6 (bottom), and 1.2 nM of different Listerin mutants showing nascent chain-tRNA (NC-tRNA) and poly-ubiquitinated substrate (poly-Ub). (F) Autoradiography of 2 min ubiquitination reactions containing 80S-RNCs, ubiquitination reagents, energy, splitting factors, 1.2 nM of either wild-type (WT) or KR-DD Listerin, and either 1.2 nM wild-type or increasing amounts of a NEMF containing four point mutations in the residues predicted to interact with the P stalk. Nascent chain-tRNA (NC-tRNA) and poly-ubiquitinated substrate (poly-Ub) are indicated. See also Table S3.

Figure 7

Working Model for Step-Wise Assembly of RQC Ubiquitination Complex Translationally stalled 80S ribosomes, which are inaccessible to both Listerin (orange) and NEMF (teal) binding, are split into subunits by the factors Pelota, Hbs1, and ABCE1 (not displayed). Ribosome splitting exposes the peptidyl tRNA of a trapped nascent chain within the 60S subunit. At this stage, Listerin can potentially bind, but is competed by 40S reassociation and a dynamic P stalk (P). By contrast, NEMF specifically recognizes and binds the peptidyl tRNA-60S interface via its globular N- and C-terminal lobes. Upon binding the 60S-tRNA interface, the coiled coil and M-domain of NEMF bind and stabilize the P stalk in a defined position. This generates an improved binding site for the N terminus of Listerin between NEMF and the 60S, facilitating docking of its C-terminal RWD domain. The ribosome-bound RWD domain positions the ligase domain at the nascent chain exit tunnel, leading to a productive ubiquitination complex.