bims-spribo Biomed News
on Specialized ribosomes
Issue of 2026–10–18
eleven papers selected by
Maxim Bouvet, Università di Torino



  1. Microbiol Mol Biol Rev. 2026 Oct 14. e0034625
      SUMMARYProtein synthesis by ribosomes proceeds through the sequential stages of initiation, elongation, termination, and ribosome recycling. In most bacteria, coupled transcription-translation enhances the efficiency of transcription but limits opportunities to repair or eliminate faulty mRNAs, thereby increasing the likelihood that ribosomes encounter incomplete or damaged transcripts. Furthermore, mRNA integrity can be compromised by transcriptional errors, abortive transcription, nucleolytic cleavage, or chemical damage. Translation of such defective transcripts, as well as other hard-to-translate mRNAs, can impede elongation or termination, resulting in stalled ribosome complexes that sequester ribosomes and tRNAs, thereby reducing their availability for subsequent rounds of translation. To maintain translation capacity, bacteria employ dedicated ribosome rescue and quality control pathways that resolve stalled complexes and promote the turnover of aberrant mRNAs and nascent polypeptides. Here, we summarize the molecular mechanisms underlying bacterial ribosome stalling, describe the pathways that rescue stalled ribosomes, and discuss current technologies for detecting ribosome stalling. We also highlight the physiological roles of programmed ribosome stalling and explore the potential of ribosome rescue pathways as druggable sites.
    Keywords:  ABCF; RQC; Ribo-seq; antibiotic; ribosome collision; ribosome profiling; ribosome stalling; tmRNA; translation arrest
    DOI:  https://doi.org/10.1128/mmbr.00346-25
  2. Sci Adv. 2026 Oct 16. 12(42): eaef7741
      Ribosomal RNA modification enzymes increase cellular fitness, but it's little known whether this benefit arises from rRNA modification or a chaperone function of the modification enzyme. Here, we show that E. coli methyltransferase RsmB chaperones the initial recruitment of ribosomal proteins to the 16S 3' domain rRNA, a key step in assembly of the 30S subunit. Real-time single-molecule assembly experiments show that the RsmB product, 16S m5C967, has little effect on the rRNA affinity for ribosomal proteins. Instead, RsmB facilitates stable recruitment of primary protein uS7 during transcription while blocking the addition of secondary protein uS19. Completion of the methyltransferase cycle promotes RsmB release, allowing assembly to continue. Dimethyl sulfate footprinting of trapped RsmB-rRNA complexes revealed that RsmB restructures a critical rRNA helix junction. Our results illustrate how an RNA modification enzyme favors the proper sequence of protein addition by temporarily reshaping the energy landscape of co-transcriptional rRNA folding.
    DOI:  https://doi.org/10.1126/sciadv.aef7741
  3. Semin Hematol. 2026 Sep 16. pii: S0037-1963(26)00087-9. [Epub ahead of print]
      Translational control has emerged as a critical layer of gene expression reprogramming in cancer, with the ribosome functioning as a central regulatory node rather than a passive protein synthesis machinery. This review provides an integrated overview of how defects in ribosomes and translational regulation contribute to the pathogenesis of lymphoid leukemias and lymphomas. We focus on 3 major axes: mutations in ribosomal proteins, alterations in ribosomal RNA, and dysregulation of translation initiation mediated by the eukaryotic initiation factor 4F complex. Recurrent mutations in ribosomal proteins, such as RPL10 in T-cell acute lymphoblastic leukemia and RPS15 in chronic lymphocytic leukemia, alter ribosome function, leading to selective changes in mRNA translation, impaired translational fidelity, and increased oxidative stress that promotes genomic instability. In parallel, emerging evidence indicates that alterations in ribosomal RNA, including changes in ribosomal DNA copy number, biogenesis, and epigenetic modifications, contribute to ribosome heterogeneity and oncogenic transformation, although their precise roles in hematologic malignancies remain incompletely understood. Furthermore, aberrant activation of translation initiation pathways-often driven by the AKT/mTOR/MYC signaling axis-enhances both global protein synthesis and selective translation of oncogenic transcripts, reinforcing malignant phenotypes. Together, these ribosome-intrinsic and -extrinsic defects converge to reprogram the translatome, promote tumor progression, and create therapeutic vulnerabilities. Targeting translational control mechanisms therefore represents a promising strategy for the treatment of lymphoid malignancies.
    Keywords:  Chronic lymphocytic leukemia; Ribosomal protein mutations; Ribosome biogenesis; T-cell acute lymphoblastic leukemia; eIF4F; rRNA
    DOI:  https://doi.org/10.1053/j.seminhematol.2026.09.002
  4. J Mol Biol. 2026 Oct 12. pii: S0022-2836(26)00438-9. [Epub ahead of print] 170065
      Ribosome biogenesis is a highly coordinated pathway that involves the assembly of ribosomal RNAs (rRNAs) with ribosomal proteins (r-proteins) to generate functional ribosomal subunits (r-subunits). The Saccharomyces cerevisiae (yeast) large 60S r-subunit consists of three rRNA molecules and 46 r-proteins. The contributions of nearly all r-proteins of the yeast large r-subunit have been characterized; however, a few non-essential proteins remain poorly understood. Although non-essential, human eL22 has been identified as a key player in p53 regulation during ribosomal stress and as a highly mutated target in cancers. Despite this function, the role of eL22 in ribosome maturation is still ill-defined. In this study, we characterized yeast eL22 r-protein, which is encoded by two paralogous genes that exhibit markedly different expression levels. Our results show that eL22 assembles into intermediate nucleolar pre-60S ribosomal particles. Loss of eL22 impairs cell growth and reduces 60S r-subunit accumulation, phenotypes that are exacerbated at low temperatures. Analysis of pre-rRNA processing by pulse-chase labeling, northern blot hybridization, and primer extension reveals a defect in 27S pre-rRNA maturation, specifically at the level of 27SB pre-rRNA processing. Consequently, nuclear export of eL22-deficient pre-60S particles is mildly impaired. Furthermore, we identify genetic interactions between eL22 and neighboring r-proteins, eL38 and eL31. We conclude that eL22 assembly is required for optimal pre-60S maturation during middle nucleolar stages, particularly at low temperatures, a function likely supported by the cooperative action of other r-proteins associated with common elements of 25S rRNA.
    Keywords:  60S ribosomal subunit; eL31; eL38; nucleolus; rRNA processing; ribosomal RNA domain III; ribosome assembly; yeast
    DOI:  https://doi.org/10.1016/j.jmb.2026.170065
  5. Cell Rep. 2026 Oct 13. pii: S2211-1247(26)01204-0. [Epub ahead of print]45(10): 118125
      Various ribosome-associated quality control pathways safeguard translation fidelity by detecting and resolving aberrant translation events. Recently, a pathway that senses stalled ribosomes with an occluded A-site has been described. The small molecules NVS1.1 and ternatin-4 induce ribosome stalling by trapping eukaryotic release factor 1 (eRF1) and elongation factor 1A1 (eEF1A1), respectively, within the ribosomal A-site, thereby promoting their ubiquitination and proteasomal degradation. Additionally to the previously identified factors GCN1, RNF14, and RNF25, we identify here the deubiquitinase USP9X as a regulator of this pathway. In the absence of USP9X deubiquitinase activity, eRF1 is still ubiquitinated but fails to undergo efficient degradation. However, compared with wild-type cells, K6-linked ubiquitin chains accumulate on eRF1 in cells lacking USP9X activity, suggesting that USP9X trims K6-linked ubiquitin chains during a late step of substrate processing. Furthermore, clearance of trapped eRF1 engages a feedback mechanism involving 4EHP and the integrated stress response (ISR) to suppress translation, whereas impaired degradation prevents translational shutdown.
    Keywords:  CP: molecular biology; K6-linked ubiquitination; USP9X; deubiquitination; eEF1A1; eRF1; proteasomal degradation; ribosome; ribosome quality control; translation; ubiquitination
    DOI:  https://doi.org/10.1016/j.celrep.2026.118125
  6. bioRxiv. 2026 Sep 30. pii: 2026.09.29.755503. [Epub ahead of print]
      Protein synthesis declines with age across many tissues, but whether this decline actively contributes to physiological aging remains unclear. Oocytes may be particularly vulnerable because they rely on ribosomes synthesized during growth and maintained for prolonged periods without continual replacement. Here we show that declining translational capacity is a causal component of oocyte aging. An unbiased genetic screen identified ribosome dosage as a major determinant of oocyte longevity, and experimentally reducing ribosome abundance was sufficient to accelerate the loss of developmental competence and prematurely recapitulate meiotic defects that arise during natural aging, while also producing defects in early embryonic development. Ribosomes isolated from aged Drosophila oocytes exhibit ~50% lower translational activity despite only a modest reduction in ribosome abundance and preserved gross structure and composition, with both ribosomal subunits contributing to this functional decline. Protein synthesis also declines markedly in aged metaphase-I mouse oocytes. Together, these findings identify long-lived translational machinery as an intrinsic vulnerability of the oocyte and establish declining ribosome function as a mechanistic contributor to reproductive aging.
    Keywords:  Fertility; aging; meiotic spindle; oocyte; ribosome; translation
    DOI:  https://doi.org/10.64898/2026.09.29.755503
  7. bioRxiv. 2026 Sep 28. pii: 2026.09.26.754687. [Epub ahead of print]
      Ribosome malfunction has toxic consequences, but how mammalian cells select ribosomal subunits for degradation remains poorly understood. Here, we develop a pulse-chase CRISPR screening strategy to identify regulators of ribosome turnover and uncover that loss of protein UFMylation promotes ribosome degradation. Normal UFMylation releases the 60S subunit from the endoplasmic reticulum (ER) translocon. Without UFMylation, single-molecule tracking and optogenetic proximity labeling reveal accumulation of ER-associated 60S subunits and their specific degradation. This translocon-associated large subunit degradation (TLSD) is independent of the lysosome and, in our human cell model, is only active in nondividing, contact-inhibited cells. Degradation requires the poorly characterized protein R3HDM4, which we term TLSD1. Upon UFMylation loss, TLSD1 redistributes to the ER and promotes 60S degradation. These findings identify a cell-state-dependent pathway for clearing ER-retained 60S subunits. We propose translocon release acts as a checkpoint for ribosome function, explaining TLSD1's genetic links to neuronal health and erythropoiesis.
    DOI:  https://doi.org/10.64898/2026.09.26.754687
  8. Sci Adv. 2026 Oct 16. 12(42): eaee5884
      In most cells, Malat1 long noncoding RNA localizes to the nucleus where it affects splicing and chromatin function. In mouse neurons, Malat1 is exported to the cytoplasm where it is translated to generate the M1 micropeptide. Here, we characterize an internal ribosome entry site (IRES) required for M1 translation that is sufficient to induce cap-independent expression of a downstream open reading frame. In vivo chemical probing and structural modeling defined a three-stem-loop RNA secondary structure that encompasses the active IRES segment and coincides with a mouse B1 SINE (short interspersed element) repetitive element. In affinity purification experiments, a minimal IRES/B1 RNA selectively bound ribosomal subunits, translation factors, and the known IRES cofactors Rack1 and hnRNP A2/B1. Depletion of Rack1 and hnRNP A2/B1 inhibited IRES-dependent translation of the reporter and expression of the endogenous M1 peptide. Our study identifies an unexpected functional unit hidden within a widely studied long noncoding RNA.
    DOI:  https://doi.org/10.1126/sciadv.aee5884
  9. Proc Natl Acad Sci U S A. 2026 Oct 20. 123(42): e2604945123
      It is well established in yeast and animal system that the level of uridine thiolation at position 34 of tRNA anticodon loops can impact the decoding potential of the corresponding codons. Using Arabidopsis thaliana, we confirm that the ability of the plant ribosome to decode AAA, GAA, and CAA codons is impaired when this thiol group is lost, leading to a reduction in protein production, especially for genes enriched in these codons. Interestingly, we observed that loss of tRNA thiolation results in variations in the levels of numerous proteins involved in sulfur-compound metabolism and amino acid biosynthesis. These variations, in turn, affect the accumulation of several sulfur-containing metabolites and amino acids, suggesting that the level of tRNA thiolation has a direct and profound impact on plant metabolism. We also demonstrate that U34 thiolation is essential for adjusting plant growth in response to sulfur limitation and that its absence directly affects the plant's interaction with bacteria, including both pathogens and beneficial organisms. Our results support the hypothesis that the level of tRNA thiolation can be used in plant to link nutritional status to translation.
    Keywords:  epitranscriptomics; plant nutrition; plant-bacteria interactions; ribosome dynamics; tRNA
    DOI:  https://doi.org/10.1073/pnas.2604945123
  10. Cell. 2026 Oct 15. pii: S0092-8674(26)01184-0. [Epub ahead of print]
      Coleoid cephalopods exhibit the highest levels of adenosine deaminases acting on RNA (ADAR)-mediated RNA editing of any known taxon, yet the functional consequences of most recoding events remain unclear. Here, we integrated proteomics with biochemical and cellular assays to characterize recoding across the Doryteuthis pealeii proteome. This confirmed the translation of 7,997 recoded sites at the protein level and revealed how recoding reshapes the proteome by altering protein stability, subcellular localization, post-translational modifications, and enzymatic activity. We find that recoding also creates or ablates post-translational modification sites, with direct effects on protein function and protein-protein interactions. Recoding the E3 ligase MARCHF5 drives widespread changes in substrate ubiquitylation and perturbs mitochondrial homeostasis, illustrating how RNA editing can influence organelle function. Together, these data give a proteome-scale view of how extensive RNA recoding diversifies protein function in coleoid cephalopods and offer a framework for understanding how RNA-level plasticity shapes protein function and cellular physiology.
    Keywords:  ADAR; MARCHF5; RNA editing; cephalopods; coleoids; post-translational modifications; protein recoding; proteomics; solvent shift; subcellular localization
    DOI:  https://doi.org/10.1016/j.cell.2026.09.043
  11. Nat Chem Biol. 2026 Oct 13.
      Ribosome biogenesis is highly upregulated in cancer and essential for malignant growth, yet efforts to selectively target this process pharmacologically have been unsuccessful. Here we identify nuclear valosin-containing protein-like (NVL), a hexameric AAA+ ATPase required for large ribosomal subunit (60S) assembly, as a druggable target in this pathway. Using forward genetics, we discovered that the cytotoxic dibenzothiazepinone MM17 inhibits NVL. Mutations conferring resistance to MM17 in cancer cells also rendered recombinant NVL refractory to enzymatic inhibition in vitro, providing convergent genetic and biochemical evidence of target engagement. Cryo-electron microscopy structures revealed two MM17-binding sites within the NVL hexamer, with resistance mutations clustering around the ligand pocket. NVL inhibition disrupts 60S biogenesis and activates p53 without inducing DNA damage. A more potent, bioavailable analog, MM927, recapitulates these effects and suppresses tumor growth in vivo without detectable toxicity. These findings establish NVL inhibitors as first-in-class therapeutics targeting ribosome biogenesis in cancer.
    DOI:  https://doi.org/10.1038/s41589-026-02324-9