Olivier Namy 🧬🧪

GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling During nutrient deprivation, activation of the protein kinase GCN2 regulates cell survival and metabolic homeostasis. In addition to amino acid stress, GCN2 is activated by a variety of cellular stres...

Beautiful reconstitution of amino acid stress-dependent ISR activation by my @harvardcellbio.bsky.social colleagues presenting a unifying mechanism for GCN2 activation, which requires ribosome collisions and is enhanced by cognate uncharged tRNA in the A site! www.science.org/doi/10.1126/...

The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking Nature Structural & Molecular Biology, Published online: 19 September 2025; doi:10.1038/s41594-025-01676-5By studying dynamic folding intermediates on the human ribosome, Pellowe et al. show that newly made domains help each other to fold but do not stably interact until synthesis is complete, avoiding interdomain misfolding.

New online: The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking

Thank you zeynep. It’s very interesting and useful. 👍

#RNAsky #RNAbiology

Translon: a single term for translated regions - Nature Methods Nature Methods - Translon: a single term for translated regions

A large consortium of researchers introduces the term 'translon' to denote any transcriptome region that is decoded by ribosomes.

www.nature.com/articles/s41...

Protocol for Disome-seq to identify transcriptome-wide ribosome collisions in yeast cells When translation elongation is hindered, stalled ribosomes can collide with trailing ribosomes and form ribosome collision complexes also known as disomes. Disomes are sensed in the cell to trigger signaling events, and therefore it is important to determine their frequency and distribution across transcripts. Here, we provide the protocol for Disome-seq in Saccharomyces cerevisiae (yeast) cells to enable transcriptome-wide detection of disomes. We describe the steps for yeast growth and isolati...

Protocol for Disome-seq to identify transcriptome-wide ribosome collisions in yeast cells #protocol #starprotocols #cellpress

An RNA modification prevents extended codon-anticodon interactions from facilitating +1 frameshifting - Nature Communications tRNAs contain many chemical modifications that regulate their function. Integrating smFRET and cryo-EM approaches, this work demonstrates that m1G37 in tRNAProL stabilizes its conformation in the ribo...

An RNA modification prevents extended codon-anticodon interactions from facilitating +1 frameshifting #rnasky #microsky 🦠 m1G (TrmD) at position 37 modulates tRNA conformation on ribosome and suppresses +1 FS induced by tRNA-Pro (four base pair codon-anticodon)💫 smFRET & cryo doi.org/10.1038/s414...

RNA modifications digest Summer 2025 Bimonthly newsletter: RNA modifications and related topics, mostly in bacteria. Summer 2025, first issue!

🦠 Launching a bimonthly digest on RNA modifications and related topics in bacteria!🤩 First issue: Summer 2025. Shared here + by email, future ones will be quicker reads! 😅 #rnasky #microsky #ribosome Subscribe and share if you are interested! rnamodifupdates.substack.com/p/rna-modifi...

Methylation of Cytidine 1407 Increases the Lifetimes of the A-Site Ground and Excited States of E. coli 16S Ribosomal RNA The C5 methylation of cytidine 1407 (C1407) in the E. coli 16S rRNA is a permanent modification. The methylation occurs directly at the A-site internal loop, a known dynamic hotspot in helix 44 (H44) ...

"C5 methylation of C1407 functions as a kinetic regulator in the E. coli rRNA to properly adjust the time frame for the selection of the correct tRNA–mRNA interaction" #rnasky #microsky #ribosome 🦠 pubs.acs.org/doi/10.1021/...

Frameshifting Stimulatory Sequence Induces Large Structural Change of Ribosomal Proteins When Bound to E. coli Ribosomes pubmed.ncbi.nlm.nih.gov/40788995/ #cryoEM

Ultra-parallel ribosome profiling platform with RNA-dependent RNA amplification Translation regulation plays a pivotal role in the diversification of gene expression and the response to intra- and extracellular environmental cues. Ribosome profiling (or Ribo-Seq) serves as a sens...

Researchers developed a high-throughput ribosome profiling method using RNA amplification that works with tiny samples.

Applied to 70 COVID-19 patients, it revealed symptom severity links to mitochondrial translation decline and stop codon readthrough.

www.biorxiv.org/content/10.1...

Free tRNALeu shows flexible variable arm and CCA end, reshaped by LeuRS and ribosome binding #tRNA #StructuralBiology bit.ly/45PxJF5

Finally out!
I’m thrilled to share our new paper (Wolin et al., Cell 2025).

This paper describes SPIDR, a high-throughput method for mapping RBP binding sites.

By combining #SPIDR with #cryoEM, we identified the exact binding site of LARP1 within the #mRNA channel of the 40S ribosomal subunit.

Editor's Pick: Shen, Ye et al. review recent literature on the role of bacterial ribosome heterogeneity on facilitating rapid response to stress.
journals.asm.org/doi/10.1128/...
@asm.org #JBacteriology

Structure of an archaeal ribosome reveals a divergent active site and hibernation factor - Nature Microbiology Sequence and structural analyses reveal a divergent peptidyl transferase centre and a hibernation factor in archaea.

Structure of an archaeal ribosome reveals a divergent active site and hibernation factor | Nature Microbiology https://www.nature.com/articles/s41564-025-02065-w

Insights on how ribosomal RNA modification distant from drug binding site can still affect drug binding, in mycobacterium 🦠 #rnasky #ribosome #microsky

Pan-viral ORFs discovery using massively parallel ribosome profiling Defining viral proteomes is crucial to understanding viral life cycles and immune recognition but the landscape of translated regions remains unknown for most viruses. We have developed massively para...

Pan-viral ORFs discovery using massively parallel ribosome profiling www.science.org/doi/10.1126/...

Mechanism of release factor–mediated peptidyl-tRNA hydrolysis on the ribosome Translation termination is essential in all living organisms because it ensures that proteins have lengths strictly defined by their genes. This universal process is mediated by peptide release factor...

www.science.org/doi/10.1126/... le 🦠💫💫💫 #ribosome #rnasky

Ribosomes modulate transcriptome abundance via generalized frameshift and out-of-frame mRNA decay Zhang et al. identify a regulatory mechanism for how cells adapt to nutrient scarcity through widespread −1 ribosomal frameshifts, culminating in accelerated mRNA decay. This process, dependent on codon optimality and conserved across species, establishes direct feedback coupling the translation of new proteins with the stability of the mRNA that encodes for them.

Ribosomes modulate transcriptome abundance via generalized frameshift and out-of-frame mRNA decay

RIOK3 mediates the degradation of 40S ribosomes Huang et al. identify a pathway for stress-induced 40S ribosome degradation: 40S ribosomes ubiquitylated by RNF10 are subsequently bound by the atypical kinase RIOK3, which mediates their degradation ...

RIOK3 mediates the degradation of 40S ribosomes: Molecular Cell www.cell.com/molecular-ce...

The cover of the April issue of @cp-trendspharma.bsky.social. Gregory Howard and William Tansey review the current status, challenges, and future prospects of cancer treatments that target the ribosome. Aberrant ribosome production and function are hallmarks of cancer.

Nouvelle facette de la protéine Rqc2, sous-unité d’un système de sauvetage des ribosomes chez Saccharomyces cerevisiae Les cellules utilisent de nombreux mécanismes de contrôle-qualité au cours de la biosynthèse des protéines. Les défauts qui perturbent le décodage de l'ARN messager peuvent provoquer le blocage des ribosomes, empêchant l'expression des gènes. Ces ribosomes bloqués ne sont plus disponibles pour le processus de traduction, ce qui représente un défi à la fois pour l'homéostasie des ribosomes et la survie de la cellule.   Les cellules eucaryotes évitent l'accumulation de polypeptides aberrants potentiellement toxiques et maintiennent la disponibilité des ribosomes en employant des mécanismes de surveillance, comme le complexe de contrôle-qualité associé aux ribosomes (RQC), très conservé au cours de l'évolution. Les voies de sauvetage dissocient le ribosome bloqué, en libérant la sous-unité 40S attachée à l'ARNm et la sous-unité 60S encore attachée à un ARNt avec le peptide en élongation. RQC assure l'ubiquitination, l'extraction et la dégradation du peptide naissant aberrant. En particulier, Rqc2p recrute, à la même position que l’ARNt au site A, des ARNt chargés en alanine et en thréonine, formant des extensions C-terminales composées de ces résidus (CAT-tails). Ces CAT-tails peuvent exposer des résidus lysine cachés dans le tunnel de sortie de la 60S pour l’ubiquitination par la E3 ligase Ltn1.   En utilisant un crible génétique, les scientifiques de l’équipe Génomique, Structure et Traduction à l’I2BC (CNRS/CEA/UPSaclay, Gif-sur-Yvette) ont identifié un allèle mutant de RQC2 comme impliqué dans la libération des peptides à partir des ribosomes bloqués. Ils ont caractérisé la protéine mutante sur le plan biochimique et, en collaboration avec l’équipe de Reynald Gillet (IGDR, Université de Rennes), sur le plan structurel, en déterminant comment la mutation ponctuelle réduisait le recrutement de l'ARNt au site A, limitant ainsi la formation des CAT-tails.   Ces résultats, publiés dans Structure, permettent de mieux comprendre le rôle de Rqc2p dans le complexe de contrôle-qualité associé aux ribosomes, et le maintien de l'homéostasie des ribosomes.   -> Contact : celine.fabret@i2bc.paris-saclay.fr

Nouvelle facette de la protéine Rqc2, sous-unité d’un système de sauvetage des ribosomes chez Saccharomyces cerevisiae

Congratulations to all the candidates who qualified for the #CNRS #CRCN competition in #Section21. Such brilliant science and incredible enthusiasm! Keep it up!

c3n-cn.fr/2025/01/31/c...

This work has been done at #I2BC @cnrsbiologie.bsky.social @cnrs-paris-saclay.bsky.social @i2bcparissaclay.bsky.social

Using cryoEM we observed This mutation promotes a misplacement of tRNA in the 60S altering the formation of #CATtails.

We performed a genetic screen to identify factor involved in the release of peptide from stalled #ribosomes. We identified a new mutation in #RQC2 factor.

RQC2 is a major player in peptide release from stalled ribosomes - PubMed Eukaryotic cells prevent the accumulation of potentially toxic aberrant polypeptides and maintain ribosome availability through surveillance and clearance mechanisms, including the evolutionarily cons...

A new publication from my lab a great work done with fantastic colleagues from #IGDR (Reynald Gillet’s team for all the cryoem work. pubmed.ncbi.nlm.nih.gov/40187343/

🚨New paper!🚨

A comprehensive take on the origins and evolution of translation factors & how these essential players evolved across the tree of life. 🌍🧬

Led by Evrim Fer @uwmadisonmdtp.bsky.social grad student! 👏

Free access: www.sciencedirect.com/science/arti... @cp-trendsgenetics.bsky.social

Structurally heterogeneous ribosomes cooperate in protein synthesis in bacterial cells - Nature Communications Cells can simultaneously produce structurally dissimilar ribosomes, suggesting functional specialization of distinct ribosome populations. Here, the authors show that distinct ribosomes cooperate rath...

Out just now @naturecomms.bsky.social: using cryo-EM and cryo-electron tomography, we provide evidence that structurally heterogeneous ribosomes can cooperate in protein synthesis in bacterial cells:

www.nature.com/articles/s41...

Transfer RNA acetylation regulates in vivo mammalian stress signaling An ancient tRNA modification is used by mammalian cells to coordinate protein translation and adaptive signaling.

Excited to share this one! We developed an in vivo model for specific manipulation of transfer RNA acetylation and found it serves as a sentinel modification whose loss causes ribosome stalling and stress signaling. Implications for a genetic disorder and cancer.

www.science.org/doi/10.1126/...