bims-spribo 2026-09-13 papers

bims-spribo

Biomed News

on Specialized ribosomes

Issue of 2026–09–13
nine papers selected by
Maxim Bouvet, Università di Torino

eIF5A and polyamines restrict mRNA levels in response to ribosome stalls.
Ribosome stalling position, spacing, and A-site occupancy impact translation and cotranslational mRNA decay in plants.
The alarmone pGpp inhibits translation through GTP depletion.
Ribosome dynamics at the conserved PGP motif governs 2A peptide-bond-skipping efficiency.
Nucleolar dynamics are determined by the ordered assembly of the ribosome.
Peroxiredoxin 1 safeguards the nucleolar genome from oxidative damage.
18S rRNA 3' end cleavage by the phosphorylated endoribonuclease NOB1 is interconnected with early small subunit biogenesis.
uORF-mediated translational control of CAK and Cdk activation in response to low nutrients in yeast.
The RNA helicase domain of NAT10 promotes the biogenesis of hypomodified ribosomes to enhance cancer cell proliferation.

Proc Natl Acad Sci U S A. 2026 Sep 15. 123(37): e2533876123

eIF5A and polyamines restrict mRNA levels in response to ribosome stalls.

Chloe M Wohlenberg, Parissa C Monem, Natalia Barbosa, Judith Frydman, Joshua A Arribere.

  Obstacles to translation elongation stall ribosomes and allow deleterious proteins to accumulate, which threatens cellular health. Cells recognize and clear stalled ribosomes via several interrelated pathways, although the mechanisms by which cells distinguish stalled from normally elongating ribosomes and mount an appropriate response are incompletely understood. While recent work highlights how ribosome collisions help cells to recognize stalled ribosomes, how other factors contribute to detection remains unclear. Here, we report a requirement for the translational factor eIF5A in the mRNA decay response to ribosomal stalling, i.e., No-Go mRNA Decay (NGD). We identified the Caenorhabditis elegans polyamine transporter, catp-6, via a forward genetic screen as a factor required for NGD. During our mechanistic dissection of the catp-6 phenotype, we uncovered a role for cellular polyamines and the translation elongation factor eIF5A in NGD, and we show this requirement is conserved from C. elegans to Saccharomyces cerevisiae. Our analyses support the idea that cells use eIF5A to identify ribosomal stalls and execute NGD and uncover a molecular function for a core protein synthesis factor in limiting expression from stall-inducing mRNAs. Our work offers insight into how cells identify and remove problematic mRNAs from the translational pool. Our work also raises the possibility that dysregulated mRNA decay is an unrecognized pathophysiology associated with polyaminopathies and eIF5A disorders, of relevance to varied neurodegenerative and aging phenotypes and efforts to pharmacologically inhibit eIF5A.

Keywords:  NGD; PARK9; eIF5A; polyamine; ribosome

DOI:  https://doi.org/10.1073/pnas.2533876123
Proc Natl Acad Sci U S A. 2026 Sep 15. 123(37): e2617633123

Ribosome stalling position, spacing, and A-site occupancy impact translation and cotranslational mRNA decay in plants.

Sjors van der Horst, Joseph L Gage, Julia Bailey-Serres.

  Ribosomes can pause during mRNA translation, but what causes pausing, how pauses affect protein production, and whether they trigger cotranslational mRNA decay are poorly understood in plants. Here, we investigate the causes and consequences of ribosome pausing in Arabidopsis and maize. This is accomplished by sizing, mapping, and quantifying footprints of individual ribosomes (monosomes) and closely spaced ribosome pairs (disomes) at single-codon resolution on open reading frames (ORFs). Ribosome footprinting was combined with 5'P-degradome-seq to examine the coincidence of pausing with cotranslational decay under control conditions and brief hypoxia in Arabidopsis. The data resolve two monosome conformations and three disome configurations. These include monosomes with a vacant or occupied A-site and disomes that have collided or are separated by one or two codons. Pausing is prevalent at initiation, termination, and di-Proline codons. Di-Proline pauses do not trigger cotranslational decay but appear important in cotranslational protein processing. Brief hypoxia induces stalling of A-site vacant ribosomes at Aspartate codons, often coinciding with 5'P peaks, indicating that rate-limiting decoding can trigger cotranslational mRNA decay. Notably, actively transcribed and translated hypoxia-response mRNAs accumulate 1- to 2-codon-separated disomes and are actively degraded. Comparative analysis of footprints in the two species reveals ribosome conformations and codon-specific pausing can be conserved or lineage-specific, as exemplified by pausing at di-Prolines and on Conserved Peptide upstream ORFs. In sum, the stalling of ribosomes at specific codons, coupled with ribosome A-site occupancy and disome spacing, modulates protein production and cotranslational mRNA decay in plants.

Keywords:  cotranslational mRNA turnover; ribosome collision; ribosome pausing; uORF

DOI:  https://doi.org/10.1073/pnas.2617633123
Nucleic Acids Res. 2026 Sep 07. pii: gkag858. [Epub ahead of print]54(17):

The alarmone pGpp inhibits translation through GTP depletion.

Kevin A England, Aude Trinquier, Leah K McKinney, Jue D Wang, Heather A Feaga.

Bacteria produce the alarmone nucleotides ppGpp and pppGpp during stress to affect replication, transcription, and metabolism. ppGpp and pppGpp also attenuate translation by competitively binding translational GTPases to conserve resources during stress. Recently, pGpp was identified as a third alarmone, and important pathogens like Clostridioides difficile exclusively produce pGpp in response to stress. Despite its abundance as an alarmone, the precise role of pGpp in mediating stress responses is poorly understood. Here, we show that, while pGpp is a weaker inhibitor of protein synthesis than ppGpp and pppGpp in vitro, pGpp production in the model Gram-positive bacterium Bacillus subtilis leads to faster translation inhibition in vivo. pGpp production leads to fewer ribosomes engaged in translation and more hibernating ribosome dimers than (p)ppGpp production, suggesting that translation initiation is strongly inhibited. Additionally, pGpp production depletes cellular GTP more rapidly than (p)ppGpp production, which we show is sufficient for translation inhibition. Faster GTP depletion during pGpp production is also accompanied by more robust transcriptome remodeling. This work expands the model by which alarmones inhibit translation to include GTP depletion and demonstrates how different alarmone species exert varying effects on physiology.

DOI: https://doi.org/10.1093/nar/gkag858
Nucleic Acids Res. 2026 Sep 07. pii: gkag875. [Epub ahead of print]54(17):

Ribosome dynamics at the conserved PGP motif governs 2A peptide-bond-skipping efficiency.

Xincheng Wu, Saori Uematsu, Yan Wu, Shu-Bing Qian.

Viral 2A oligopeptides drive an unusual ribosome recoding event in which peptide-bond formation fails at a conserved PG↓P motif, producing two discrete proteins without canonical termination. Despite decades of study, the molecular basis of 2A-mediated peptide-bond skipping remains poorly understood. Here, we combine quantitative 2A reporters with high-resolution ribosome profiling to interrogate ribosome dynamics at the core 2A sequences. We identify a pausing event at the terminal proline codon of the PGP motif that functions as a kinetic decision point: ribosome dwell time at this site inversely correlates with skipping efficiency. Increasing nascent chain flexibility by inserting linkers immediately upstream of the 2A sequence reduces ribosome occupancy at the terminal proline codon and enhances peptide-bond skipping. Strikingly, amino acid repeats positioned distally upstream also modulate 2A activity, indicating long-range coupling between nascent chain properties outside of the ribosome and the peptidyl transferase center inside the ribosome. In particular, hydrophobic residues potently suppress skipping, an effect that can be rescued by extending flexible segments within the peptide exit tunnel. Together, our findings support a model in which nascent chain features-beyond the core 2A motif-dynamically tune ribosomal recoding efficiency through co-translational feedback into the catalytic center.

DOI: https://doi.org/10.1093/nar/gkag875
J Cell Biol. 2026 Nov 02. pii: e202605096. [Epub ahead of print]225(11):

Nucleolar dynamics are determined by the ordered assembly of the ribosome.

Jessica Sheu-Gruttadauria, Xiaowei Yan, Nico Stuurman, Riley O Ogrean, Sabrina Lin, Stephen N Floor, Ronald D Vale.

Ribosome biogenesis occurs in the nucleolus, a biomolecular condensate whose material properties are thought to be important for function. However, the molecular basis of nucleolar dynamics and their relationship to ribosome assembly remain incompletely understood. We present a platform for high-throughput FRAP (HiT-FRAP) and use it to screen hundreds of genes for their impact on dynamics of the nucleolar scaffold nucleophosmin (NPM1). We find that NPM1 dynamics and nucleolar morphology are sensitive to ribosome assembly state: accumulation of early pre-ribosomal intermediates slows NPM1 dynamics and compacts the condensate, while accumulation of abortive late precursors accelerates dynamics and disrupts condensate integrity. These opposing biophysical states correlate with the strength of NPM1-pre-ribosome interactions. Importantly, mutations in the NPM1 intrinsically disordered region that alter pre-ribosome binding directly tune nucleolar dynamics. These results establish that ribosomal precursor assembly state determines nucleolar material properties through the strength of scaffold-pre-ribosome interactions and introduce HiT-FRAP as a platform for interrogating condensate dynamics broadly.

DOI: https://doi.org/10.1083/jcb.202605096
Sci Adv. 2026 Sep 11. 12(37): eaed4161

Peroxiredoxin 1 safeguards the nucleolar genome from oxidative damage.

Vaibhavi Gujar, Takashi Furusawa, Shalu Sharma, Frimpong Boateng, Haojian Li, Cyrinne Achour, Daiki Taniyama, Michael Kruhlak, Yves Pommier, Shalini Oberdoerffer, Travis H Stracker, Urbain Weyemi.

Peroxiredoxin 1 (PRDX1) is a highly conserved, thiol-dependent peroxidase that rapidly scavenges reactive oxygen species to modulate redox signaling. PRDX1-null mice exhibited genomic instability, shortened life span, and accelerated tumorigenesis, including development of lymphomas, sarcomas, and carcinomas. Despite extensive characterization of these phenotypes, the molecular mechanism by which PRDX1 loss causes genomic instability remains poorly understood. Here, we show that PRDX1 deficiency alters nucleolar morphology, impairs RNA polymerase I (POL-I)-dependent transcription of pre-ribosomal RNAs, and triggers nucleolar genomic instability. This oxidative stress-induced nucleolar dysfunction promotes the stability of secondary DNA structures, such as RNA-DNA hybrids and G-quadruplex DNA, contributing to nucleolar genomic instability. We demonstrate that PRDX1 loss reduces nascent ribosomal RNA (rRNA) levels and impairs rRNA processing, further affecting ribosome biogenesis. Mechanistically, we established that PRDX1 loss triggers activation of the nucleolar DNA damage response characterized by activation of the DNA repair kinase ATM and elevated TCOF1 within the nucleolus. In addition, we observed recruitment of the MRE11-RAD50-NBS1 (MRN) complex subunit NBS1 to ribosomal DNA (rDNA) loci and this was further increased under oxidative stress. NBS1 accumulation correlates with the repression of rDNA transcription by POL-I, potentially delaying rRNA synthesis, and safeguarding the nucleolar genome from further oxidative damage. Collectively, these findings uncover a previously unrecognized, but critical role, for PRDX1 in maintaining nucleolar integrity and ribosomal biogenesis through redox-dependent regulation of rDNA transcription and processing machinery.

DOI: https://doi.org/10.1126/sciadv.aed4161
RNA. 2026 Sep 10. pii: rna.081089.126. [Epub ahead of print]

18S rRNA 3' end cleavage by the phosphorylated endoribonuclease NOB1 is interconnected with early small subunit biogenesis.

Katja I Bloch von Blottnitz, Mona Honemann-Capito, Philipp Hackert, Olexandr Dybkov, Christof Lenz, Markus T Bohnsack, Sonja Lorenz, Henning Urlaub, Claudia Schneider, Katherine E Bohnsack.

  Processing of the precursor ribosomal RNAs (pre-rRNAs) is a key aspect of ribosomal subunit assembly that is closely coordinated with other maturation events. The ribonucleases that mediate pre-rRNA cleavages require regulation to ensure that their activities are exerted in a timely manner. Post-translational modifications can influence protein functions, and although many human ribosome assembly factors are reported to be post-translationally modified, most of these sites remain unconfirmed and functional insights are lacking. Here, we show that NOB1, the PIN domain endoribonuclease responsible for cleavage of the 3' end of the 18S rRNA, is phosphorylated within an evolutionarily conserved acidic tract that can be modified by casein kinase II in vitro. Association of NOB1 with pre-ribosomes is independent of these phosphorylations, and lack of NOB1 phosphorylation only mildly perturbs the efficiency of SSU maturation events upstream of 3' end cleavage of the 18S rRNA. Interestingly, our analyses of pre-rRNA levels in cells depleted of NOB1 or lacking its catalytic activity revealed not only accumulation of the 18SE precursor of the 18S rRNA, but also altered levels of pre-rRNAs containing 5' external transcribed spacer (ETS) sequences (43S, 26S and 30S). This suggests that lack of NOB1-mediated pre-rRNA cleavage impairs recycling of assembly factors required during early biogenesis steps, leading to altered kinetics of 5' ETS processing. Taken together, these data provide new insights into the role of NOB1 during SSU biogenesis and the post-translational regulation of this ribonuclease.

Keywords:  Endoribonuclease; Phosphorylation; PilT N-terminal (PIN) domain; Ribosomal RNA processing; Ribosome biogenesis

DOI:  https://doi.org/10.1261/rna.081089.126
EMBO Rep. 2026 Sep 05.

uORF-mediated translational control of CAK and Cdk activation in response to low nutrients in yeast.

Heidi M Blank, Eun-Gyu No, Ainsley E Nelson, Abigail Payne, Sofia Lykidis, Michael Polymenis.

Cyclin-dependent kinases (Cdks) require activating T-loop phosphorylation, a modification considered constitutive. Here, we examine the regulation of the Cdk-activating kinase, Cak1, in budding yeast. We measure Cak1 levels and the activating T169 phosphorylation of Cdc28 (the budding yeast Cdk) in different nutrients. The abundance of Cak1 and T169 phosphorylation is reduced in cells that proliferate very slowly or enter quiescence. A small upstream open reading frame (uORF) in CAK1 represses Cak1 synthesis, especially in poor growth conditions. Eliminating the uORF increases Cak1 levels but does not alter proliferation kinetics under most laboratory contexts. Instead, it reduces the viability of quiescent cells. In cells lacking several type 2 C protein phosphatases, which remove the T169 phosphorylation, initiation of cell division is accelerated in the absence of the uORF in CAK1. Our results suggest an unexpected layer of control, impinging on the activating phosphorylation of the Cdk. The uORF-mediated repression of Cak1 synthesis directly couples protein synthesis to the activity of the core cell cycle machinery.

DOI: https://doi.org/10.1038/s44319-026-00916-z
Nat Commun. 2026 Aug 08. pii: 9529. [Epub ahead of print]17(1):

The RNA helicase domain of NAT10 promotes the biogenesis of hypomodified ribosomes to enhance cancer cell proliferation.

Mahmood H Dalhat, Sharath Narayan, Maria Eleftheriou, James Russell, James Heslop, Hannah Serio, Khulood A Alzahrani, Adam Suh, Ajay Edakkara, Sweta Raikundalia, Lea Landmann, Ryan Asby, Evangelia Stamou, Judith López, Yogeshkumar Malam, Demetrios Aspris, Emmely A Patrasso, Stephanie Mou, George Giotopoulos, Walid T Khaled, Brian J P Huntly, Fotios Sampaziotis, Konstantinos Tzelepis, Daniel Arango.

N-acetyltransferase 10 (NAT10) is a multifunctional enzyme that harbors RNA acetyltransferase and RNA helicase domains and has emerged as a therapeutic vulnerability in solid and hematological malignancies. By coupling Proteolysis Targeting Chimera-mediated degradation of NAT10 with a deep mutational scanning assay, followed by validations in biochemical assays, human cell lines, and female mouse xenografts, we find that the RNA helicase domain of NAT10 enhances cancer cell proliferation and tumor growth. This proliferative function of NAT10 is independent of RNA acetylation but requires its RNA-binding activity. The RNA helicase domain of NAT10 is required for 18S rRNA binding, promoting biogenesis of the 40S ribosomal subunit, while simultaneously interfering with the deposition of the conserved 18S rRNA modification m¹acp³Ψ. Loss of m¹acp³Ψ in 18S rRNA enhances cancer cell proliferation, revealing that NAT10 promotes the biogenesis of hypomodified ribosomes to facilitate tumor growth. These findings uncover a mechanism by which NAT10 promotes cancer cell proliferation and establish its RNA helicase domain as a potential therapeutic target.

DOI: https://doi.org/10.1038/s41467-026-76383-w