Messenger RNA (mRNA) homeostasis is a critical aspect of cellular function, involving the dynamic interplay between transcription and decay processes. Recent advances have revealed that the ribosome plays a central role in coordinating mRNA decay, challenging the traditional view that free mRNA is the primary substrate for degradation. This review examines the mechanisms whereby ribosomes facilitate both the licensing and execution of mRNA decay. This involves factors such as the Ccr4–Not complex, small MutS-related domain endonucleases, and various quality control pathways. We discuss how translational fidelity, as well as the presence of nonoptimal codons and ribosome collisions, can trigger decay pathways such as nonstop decay and no-go decay. Furthermore, we highlight the direct association of canonical exonucleases, such as Xrn1 and the Ski-exosome system, with the ribosome, underscoring the ribosome’s multifaceted role as a platform for regulatory processes governing mRNA stability. By integrating recent findings, this review offers a comprehensive overview of the structural basis of how ribosomes not only facilitate translation but also serve as critical hubs for mRNA decay coordination.

SUMMARY: The 5S ribosomal RNA gene is present in the human genome not once but in ∼80 copies, arranged head to tail in a single array of ribosomal DNA on chromosome 1 - one of the most repetitive and least explored regions of the genome. Its product is one of the four RNAs in every ribosome and, when ribosome assembly fails, it activates the tumour suppressor p53. Whether these copies vary in sequence between people, and whether such variation has physiological or pathological consequences, is unknown. Using telomere-to-telomere genome assemblies, whole-genome sequences from ∼490 000 UK Biobank participants, and ∼940 GTEx transcriptomes, we find that every person carries copies bearing substitutions or indels, and that ∼10% of people express such variant 5S rRNA. Mutating every position of the gene in vitro , we find that variants blocking incorporation into the ribosome map to the uL5/uL18 interface and activate p53. Remarkably, these same variants are depleted from human populations: selection has acted on the step that p53 monitors. Ribosomal DNA is thus a functional source of human genetic variation, long invisible to genome-wide analysis and shaped by the p53 pathway it controls. HIGHLIGHTS: A single chromosome-1 array makes every person a carrier of variant 5S rRNA genes Saturation mutagenesis maps 5S variants that block assembly and activate p53 Assembly-blocking variants are purged from human populations via p53 surveillance eTOC: Sengl et al. resolve sequence variation across the human 5S rDNA array, one of the genome’s least-explored regions. Variant 5S rRNAs are expressed; and variants that block ribosome assembly activate p53 and are removed from human populations by selection. Abstract Figure:

MRNAs can form stable structures that need to be resolved to facilitate translation. During translation initiation in mammals, the scanning 48S complex requires the helicase activity of DHX29 to unwind stable mRNA structures that cannot be resolved by eIF4A. Here, we show that the yeast DHX29 homolog, Ylr419w (Dhx29), has a similar function during translation on elongating 80S ribosomes. Cryo-EM analyses show that the Dhx29 helicase module is positioned at the mRNA entry channel to engage mRNA, while its double-stranded RNA-binding domain (dsRBD) senses hairpin-forming mRNA in the ribosomal A-site. By selective ribosome profiling, we observed that Dhx29 is associated with transcripts that form RNA structures, such as stable tetraloops. Dhx29 mutants with perturbed helicase activity enrich 80S with hairpins in the A-site, as well as ribosome collisions, while a mutant lacking the N-terminal dsRBD sensor domain loses the specificity for such ribosomes. We thus propose that Dhx29 functions in translation elongation by resolving structured mRNA formed in the ribosomal A-site through its 3’-5’ helicase activity and pulling on the mRNA from its 3’ end.