iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation

Abstract

Since multiple ribosomes can engage a single mRNA, nonuniform ribosome progression can result in collisions. Ribosome collisions during translation elongation elicit a multifaceted ribosome-associated quality control (RQC) response. Despite advanced mechanistic understanding of translation initiation, a parallel RQC pathway that acts on collided preinitiation complexes has not been described. Here, we show that blocking progression of scanning or elongating ribosomes past the start codon triggers uS3 and uS5 ribosomal ubiquitylation. We demonstrate that conditions that activate the integrated stress response can also induce preinitiation complex collisions. The ubiquitin ligase, RNF10, and the deubiquitylating enzyme, USP10, are the key regulators of uS3 and uS5 ubiquitylation. Prolonged uS3 and uS5 ubiquitylation results in 40S, but not 60S, ribosomal protein degradation in an autophagy-independent manner. This study identifies a distinct arm in the RQC pathway, initiation RQC (iRQC), that acts on pervasive ribosome collisions during translation initiation to modulate translation activity and capacity.

Ubiquitin-mediated mechanisms of translational control

“…RQC can occur both at the initiation stage (iRQC) and at the elongation phase of translation (canonical RQC). In this sense a translation initiation blockage caused by PIC collision activated by Integrated Stress Response (ISR) has recently been identified [61]. In these studies, stressing the cells with Thapsigargin (ISR inducing agent) or Harringtonine (an initiation-specific translation inhibitor) induces collision between the trailing 48S PIC and the stalled 80S ribosome, activating initiation Ribosome Quality Control (iRQC) by recruiting the E3 ligase RNF10 to collision sites to ubiquitinate 40S subunit ribosomal proteins uS3 and uS5.…”

“…On the contrary, if these modifications are eliminated by deubiquitinase USP10, translation and protein synthesis are resumed (Fig. 2A) [61,62].…”

Targeted protein degradation: from small molecules to complex organelles—a Keystone Symposia report

“…Together, the results suggest that a separate arm of the ribosome quality control pathway, initiation ribosome-associated quality control (iRQC), targets either terminally stalled isolated preinitiation complexes or collided preinitiation complexes for degradation. 86,89,90 Interplay between refolding and ubiquitin-mediated degradation for cytosolic and nuclear proteins Judith Frydman from Stanford University discussed how the chaperone and ubiquitin machineries communicate with each other to determine whether a misfolded protein is degraded or refolded. Frydman's group has identified chaperone/E3 ligase circuits that cooperate to target misfolded proteins for degradation by the UPS.…”

Translational buffering by ribosome stalling in upstream open reading frames

“…This dissociation could serve to maintain the free pool of 40S ribosomal subunits while still allowing regulation of main ORF translation. Collisions between scanning ribosomes and their subsequent dissociation have also recently been proposed in a model of initiation RQC 80 . Collisions between scanning and elongating ribosomes and subsequent quality control are not well understood; What we describe as scanning ribosome dissociation here may be rescue by a quality control pathway.…”

“…If we were to model cap-tethered initiation, strong uORF elongating ribosome stalls would eventually sever this connection, similar to how the cap-eIF-ribosome connection is severed during the usually longer translation of main ORFs [87][88][89] . It will be also interesting to consider the effect of cellular stress-reduced elongation rates 90 and increased re-initiation 91 , both of which might regulate uORF-mediated buffering, as well as elongating ribosome dissociation through known quality control pathways 39,80,[92][93][94][95][96] .…”