Ribosome quality control

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

The overarching goal of this project is to identify and characterize novel regulatory quality control mechanisms governing ribosomal RNA (rRNA) and transfer RNA (tRNA), and to understand how these pathways are modulated to maintain biological function and promote human health. Over the past year, we have made substantial progress in elucidating the roles of these quality control mechanisms in cancer biology and cellular stress responses. Our accomplishments are organized under two specific aims: Aim 1. Discovery and characterization of novel ribosome quality control factors A major challenge in studying rRNA quality control in mammalian systems is the technical difficulty of introducing targeted mutations into human rDNA and monitoring decay processes, owing to the complex and highly repetitive nature of rDNA operons. To overcome this, our laboratory developed a trackable, orthogonal human rRNA expression system that enables the interrogation of rRNA surveillance mechanisms. Using this system, we uncovered a negative feedback loop that fine-tunes translation initiation and promotes the ubiquitin-dependent turnover of faulty 18S rRNA. Specifically, defective 18S rRNA is incorporated into translationally competent 40S subunits, which then stall at translation initiation sites across the transcriptome. Prolonged stalling activates the integrated stress response (ISR) through GCN2 kinase. Activation of the ISR downregulates global translation initiation, limiting ribosome collisions between scanning 40S subunits and aberrant ribosomes stalled at initiation sites and enabling recognition of aberrant ribosomes by the E3 ubiquitin ligase RNF10. RNF10-mediated ubiquitination of ribosomal proteins is essential for the subsequent degradation of both 18S rRNA and associated ribosomal proteins. The atypical kinase RIOK3 then binds the ubiquitinated 40S subunits to facilitate 18S rRNA decay. These findings establish a previously unrecognized GCN2-RNF10-RIOK3 axis that governs mammalian 40S quality control. Given growing interest in ISR-targeted therapeutics, our work defines a novel role for ISR signaling in the regulation of ribosome homeostasis with potential implications for disease intervention. Aim 2: tRNA chemical modifications and links to proteome homeostasis in cancer tRNAs are essential for accurate decoding of the genetic code and are heavily modified to ensure structural integrity and functional specificity. Post-transcriptional modifications-such as methylation, acetylation, hydroxylation, and deamination-can fine-tune translation rates by altering tRNA base-pairing capacity and decoding properties. Loss of specific tRNA modifications can destabilize tRNAs, targeting them for degradation via the rapid tRNA decay (RTD) pathway. In collaboration with Jordan Meier's group, we investigated the functional consequences of losing N4-acetylcytidine (ac4C), a highly conserved tRNA modification catalyzed by the essential acetyltransferase NAT10. Our results reveal that loss of ac4C in type II tRNAs leads to decreased tRNA stability, ribosome stalling, and activation of the ISR, thereby linking tRNA modification status to stress-responsive translation control. These findings demonstrate that tRNA epigenetic marks can regulate ribosome-mediated signaling in vivo and highlight new opportunities to manipulate translation in disease. We are also examining how disruption of other non-essential tRNA modifications affects tRNA stability and proteome composition in cancer-relevant settings. This work aims to elucidate the role of tRNA modification networks in modulating translation fidelity and cellular stress responses, and to identify potential therapeutic vulnerabilities associated with defective tRNA metabolism.