Olivier Namy 🧬🧪
@onamy.bsky.social
Phd, director of research, RNA Biology & Ribosome, former president Section 21 #CNRS, #RNA and #ribosome fan, specialist in translation regulations at #I2BC ORCID: 0000-0002-1143-5961
New preprint from @novoalab.bsky.social ! Which tRNAs are used by ribosomes during translation? We introduce tRIBO-seq, a nanopore method to sequence ribosome-associated tRNAs and track how the active tRNA pool changes across stress conditions. www.biorxiv.org/content/10.6... Thread 👇
In this review, we highlight the recent innovations that have expanded the utility of ribosome profiling (Ribo-seq) to resolve distinct ribosome populations, and how these approaches advanced our understanding of translational control bit.ly/4p4aY6h
Ribosome collisions activate ZAK, influencing cell fate via p38 & JNK phosphorylation. Biochemistry & cryo-EM uncover distinct ZAK-ribosome interactions. PMID:41261136, Nature 2025, @Nature https://doi.org/10.1038/s41586-025-09772-8 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
ZAK activation at the collided ribosome | Nature
Ribosome collisions activate the ribotoxic stress response mediated by the MAP3K ZAK, which in turn regulates cell-fate consequences through downstream phosphorylation of the MAPKs p38 and JNK1. Despite the critical role of ZAK during cellular stress, a mechanistic and structural understanding of ZAK–ribosome interactions and how these lead to activation remain elusive. Here we combine biochemistry and cryo-electron microscopy to discover distinct ZAK–ribosome interactions required for constitutive recruitment and for activation. We find that upon induction of ribosome collisions, interactions between ZAK and the ribosomal protein RACK1 enable its activation by dimerization of its SAM domains at the collision interface. Furthermore, we discover how this process is negatively regulated by the ribosome-binding protein SERBP1 to prevent constitutive ZAK activation. Characterization of novel SAM variants as well as a known pathogenic variant of the SAM domain of ZAK supports a key role of
doi.org
A (belated!) highlight from an excellent collaboration with @dunhamlab.bsky.social and #HouLabTJU. In this Nat Commun paper, we combine smFRET and cryo-EM to show how the tRNA modification m¹G37 stabilizes the reading frame—and what happens when it’s missing.
Cells maintain protein synthesis quality by allowing more efficient ribosomes to outcompete and trigger the removal of less efficient ones, supporting cellular accuracy and resilience.
Cells reveal 'survival of the fittest' through ribosome competition
Ribosomes—the tiny factories that build proteins in our cells—don't all work with the same efficiency. Researchers from Japan have discovered that ribosomes actually compete with one another, and those that perform poorly are selectively broken down when more efficient ones are present.
phys.org
I am very pleased to share our latest article published in NAR Genomics and Bioinformatics. A collaborative effort with great colleagues from the I2BC NGS facility. thanks to @i2bcparissaclay.bsky.social for its financial support through epiRNA programs academic.oup.com/nargab/artic...
High-resolution HIV-1 m6A epitranscriptome reveals isoform-dependent methylation clusters and unique 2-LTR transcript modifications
Abstract. The N6-methyladenosine (m6A) modification of HIV-1 has been widely studied but the number and precise positions of the m6A sites remain unclear d
academic.oup.com
This is a very interesting reaction catalyzed by a radical SAM enzyme on the ribosome (plus uses methyl cobalamin). Hypoxia-induced ribosomal RNA modifications in the peptidyl-transferase center contribute to anaerobic growth of bacteria: Molecular Cell www.cell.com/molecular-ce...
Hypoxia-induced ribosomal RNA modifications in the peptidyl-transferase center contribute to anaerobic growth of bacteria
Ishiguro et al. identify stereoselective ribose-backbone methylations in the peptidyl-transferase center of E. coli ribosomes, installed by the cobalamin-dependent enzyme RlmX. These methylations, tog...
cell.com
Over the weekend, Molecular Genetics and Genomics published our most recent paper. Upstream start codons can produce alternative proteins with novel N-terminal amino acids that block signal peptides. These proteins are translated but not found in any proteomics experiments. rdcu.be/eUi7o
The degradation of extended protein isoforms points to a misfiring translation initiation process
rdcu.be
Our new paper on DusB’s role in redox metabolism in V. cholerae is now out in @narjournal.bsky.social linking tRNAmodif enzymes and metabolic adaptation. Beyond RNA modification: a tRNA-modifying enzyme shaping oxidative stress resilience and metabolism in V. cholerae #rnasky #rnabiology 😊🦠💫
Beyond RNA modification: a novel role for tRNA modifying enzyme in oxidative stress response and metabolism
Abstract. RNA modifications play a fundamental role in regulating essential cellular processes, including translation fidelity and stress adaptation. While
academic.oup.com
In the New and Notable "tRNA selection in eukaryotes: A new twist in a familiar tale," Moumita Dey and Alexey Petrov highlight the paper "Near-Cognate tRNAs Enhance tRNA Rejection and Prime the Ribosome for Rapid Subsequent tRNA Testing."
tRNA selection in eukaryotes: A new twist in a familiar tale
Protein synthesis is precise, with one error per 10,000 incorporated amino acids. This is remarkable, as non-cognate and near-cognate tRNAs (tRNAs that do not match the decoded codon) outnumber…
cell.com
Using "in extracto cryo-EM", we visualize ribosomes in mammalian lysates, including RRL. "Hibernating" ribosomes carry an extended set of proteins that protect functional centers. These include elongation factor eEF2, LARP1 implicated in mTOR signaling, eIF5A etc. www.biorxiv.org/content/10.1...
Waouh translational termination depends on circadian cycle!
Cell Reports@cp-cellreports.bsky.social · 9mo agoCircadian clock control of ribosome composition promotes rhythmic translation and termination fidelity
Leoš Valášek, Julius Lukeš, Olivier Namy (@onamy.bsky.social) and Mark Osborn are among the winners of 2025 Synergy Grants. They'll investigate premature termination codons, the genetic 'stop signals' that cut production of proteins short causing disorders. 🧬🔬 👉 buff.ly/ZQhLp4h #ERCSyG
I am very proud to announce that our team has received an ERC synergy grant from @erc.europa.eu. A wonderful recognition of a truly collaborative effort with friends (Julius Lukes, Leos Valasek and Mark Osborn). Excited to begin this journey at @i2bcparissaclay.bsky.social @cnrs.fr
European Research Council (ERC)@erc.europa.eu · 9mo agoThe newly announced ERC Synergy Grant includes research on: ✴️ genetic drug design ✴️ the Big Bang's first microseconds ✴️ crowd movement ✴️ nature-society interactions 👉 buff.ly/ZQhLp4h Congrats to the 66 awarded research teams! #FrontierResearch
🎃 Trick or transcript? Bacteria rewire their RNA world under stress & infection. tRNA mods as dual-function sensors, phage tRNA slashers, hibernating ribosomes & haunted translation hubs. 🧬🧪 Full November 1st issue → #RNAmod #Epitranscriptomics #HalloweenScience #rnasky #microsky
📰 🎃 RNA Modifications Newsletter – October 31st - November 1st, 2025
Issue #5
rnamodifupdates.substack.com
Excited to announce the YAK lab's first paper and the discovery of the FIRST human cellular PRF signal to give access to two overlapping open reading frames (science.org/doi/10.1126/...)! Before we dive in, the story actually begins in a Nature from 11 years ago
Pelota, a ribosome rescue factor, unlocks the secret to longevity and age-defying health across species. This discovery sheds light on how quality control in protein synthesis can combat ... 🧵 Thread below Full analysis: https://helixbrief.com/article/a2e1736b-7031-4cdb-98d7-78309181890c
Probably one of the best European lab if you are interested in ribosome structure! Go go go
Wilson Lab@wilsonlab.bsky.social · 10mo agoWe are hiring…position suitable for PhD student with interest in ribosomes, antibiotics and cryoEM… www.uni-hamburg.de/en/stellenan...
A new family of ribosome hibernation factors in Archaea https://www.biorxiv.org/content/10.1101/2025.10.11.676729v1
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/...
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...
science.org
New online: The human ribosome modulates multidomain protein biogenesis by delaying cotranslational domain docking
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.
go.nature.com
Jack Tierney@jackatierney.bsky.social · 11mo agoMany transcriptome regions are translated but not known to encode proteins. They remain poorly annotated and thus under studied, partly due to the lack of terminology for these features. In @natmethods.nature.com we propose using "Translon" for any region decoded by the ribosome
A large consortium of researchers introduces the term 'translon' to denote any transcriptome region that is decoded by ribosomes. www.nature.com/articles/s41...
Translon: a single term for translated regions - Nature Methods
Nature Methods - Translon: a single term for translated regions
nature.com
Protocol for Disome-seq to identify transcriptome-wide ribosome collisions in yeast cells #protocol #starprotocols #cellpress
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...
dlvr.it
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...
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...
doi.org
🦠 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...
RNA modifications digest Summer 2025
Bimonthly newsletter: RNA modifications and related topics, mostly in bacteria. Summer 2025, first issue!
rnamodifupdates.substack.com
"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/...
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) ...
pubs.acs.org
Frameshifting Stimulatory Sequence Induces Large Structural Change of Ribosomal Proteins When Bound to E. coli Ribosomes pubmed.ncbi.nlm.nih.gov/40788995/ #cryoEM
