RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS

@aribio.bsky.social

In Ribosome we Trust!!! Ferreira-Cerca group at the Structural Biology of the Cell laboratory (BIOC) @CNRS / @École polytechnique More information available at https://ferreiracercalab.com/ #archaea #Ribosome #RNA

540 followers219 following17 posts

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Israel S. Fernandez
@piratefernandez.bsky.social

Today together with Prof. John McCutcheon lab @arizonastateuni.bsky.social we have visualized by cryoEM what looks like a very funky ribosome from an insect endosymbiont. We believe there are important evolutionary implications. Here the pre-print: www.biorxiv.org/content/10.6...

biorxiv.orgA mitochondrion-like ribosome in an insect endosymbiontUnderstanding how the mitochondrion evolved from a bacterial endosymbiont to an organelle is obscured by time and a lack of comparative examples. It is clear that mitochondrial ribosomes are derived f...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

César Sánchez
@twistedbacteria.bsky.social

A single archaeon couples long-chain fatty acid oxidation to methanogenesis So, "methanogens can function as primary degraders of complex organic matter, challenging the classical syntrophic paradigm" 🦠 (shareable link to read the article: rdcu.be/t3PwCaNNrEMa) www.nature.com/articles/s41...

nature.comA single archaeon couples long-chain fatty acid oxidation to methanogenesis - NatureMethanoglobus dolicholipophagus AA-75 is a thermophilic archaeon isolated from a Chinese petroleum reservoir that converts methanol into methane, carbon dioxide and acetate, and uses saturated and&nbs...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Zeynep Baharoglu
@zeynepbaharoglu.bsky.social

EF-P-resolved ribosome stalling and collision trigger Rae1-mediated mRNA decay 🦠https://www.biorxiv.org/content/10.64898/2026.10.09.757949v2 Rae1 cleaves mRNAs with ribosomes stalled on truncated transcripts lacking a stop-codon in B. subtilis

biorxiv.orgEF-P-resolved ribosome stalling and collision trigger Rae1-mediated mRNA decayRibosome stalling compromises proteome integrity and cellular fitness, and requires efficient mechanisms to eliminate problematic mRNAs and rescue blocked ribosomes. We previously identified Rae1 as an endoribonuclease that cleaves mRNAs at the tail end of stalled ribosomes to promote mRNA degradation in Bacillus subtilis. Here, we show that Rae1 has a broader role in the quality control of mRNAs that encounter translation problems. Global 5-end sequencing identified 31 previously unknown Rae1 cleavage sites, many of them associated with ribosome pausing at polyproline motifs in the absence of elongation factor P (EF-P). We also demonstrate that Rae1 cleaves mRNAs with ribosomes stalled on truncated transcripts lacking a stop-codon (non-stop mRNAs), provided that the transcript is sufficiently long to accommodate multiple collided ribosomes. Rae1 cleavage depends on a cytosine-poor context at the cut site, showing that both ribosome collisions and RNA sequence at the cleavage site govern the ability of Rae1 to promote the removal of stalled ribosomes from mRNA. ### Competing Interest Statement The authors have declared no competing interest.

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Roger Cruz-Vera
@cruzveralab.bsky.social

Great review of a hot topic! Ribosome roadblocks and traffic controllers in bacteria | Microbiology and Molecular Biology Reviews journals.asm.org/doi/10.1128/...

journals.asm.orgRibosome roadblocks and traffic controllers in bacteria | Microbiology and Molecular Biology ReviewsSUMMARYProtein 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.

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

erzbergerlab.bsky.social
@erzbergerlab.bsky.social

Ribosome remodeling drives translation adaptation during viral infection and cellular stress: Molecular Cell www.cell.com/molecular-ce...

cell.comRibosome remodeling drives translation adaptation during viral infection and cellular stressTsai et al. discover that ribosome composition is reprogrammed in response to intrinsic and external cellular perturbations, which supports ribosome remodeling as a conserved mechanism that enables ad...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Diorge Souza
@diorgeps.bsky.social

Finally out! Our work uncovers evolutionary links between bacterial and archaeal ribosome hibernation and eukaryotic energy sensing, through the archaeal hibernation factor AHA link.springer.com/article/10.1...

link.springer.comA conserved archaeal protein with evolutionary links to bacterial ribosome hibernation and eukaryotic energy sensing - The EMBO JournalRibosome hibernation helps cells survive stress by reversibly silencing translation and preserving ribosomal complexes. Although well characterized in bacteria and eukaryotes, archaeal hibernation rem...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

The EMBO Journal
@embojournal.org

How about stress-induced ribosome hibernation in archaea? @diorgeps.bsky.social, @archaeon-alex.bsky.social, Joey Davis et al identify conserved archaeal factor AHA with evolutionary link to bacterial hibernation-promoting factor HPF & eukaryotic energy sensor AMPKγ link.springer.com/article/10.1...

link.springer.comA conserved archaeal protein with evolutionary links to bacterial ribosome hibernation and eukaryotic energy sensing - The EMBO JournalRibosome hibernation helps cells survive stress by reversibly silencing translation and preserving ribosomal complexes. Although well characterized in bacteria and eukaryotes, archaeal hibernation rem...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Archaea Biology Vienna
@archaea-vienna.bsky.social

Our paper on the dynamics of Asgard archaea (Promethearchaeota) is now out in Nature! Huge thanks to the reviewers for helping make the manuscript stronger. www.nature.com/articles/s41... Two “Lokis” stained for Lokiactin (FastAct, magenta), reaching toward each other to celebrate 🎉 #archaea

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Zeynep Baharoglu
@zeynepbaharoglu.bsky.social

Ribosome profiling reveals translational dynamics between an archaeal virus and its host www.biorxiv.org/content/10.6...

biorxiv.orgRibosome profiling reveals translational dynamics between an archaeal virus and its hostHost-virus interactions remain poorly understood in archaea, whose information processing systems harbor a mosaic of bacterial and eukaryotic features. Here, we used complementary multiomics to invest...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Zeynep Baharoglu
@zeynepbaharoglu.bsky.social

16S rRNA Modifications Are Dispensable for Viability but Collectively Optimize Ribosome Biogenesis and Translation Initiation in Escherichia coli www.biorxiv.org/content/10.6...

biorxiv.org16S rRNA Modifications Are Dispensable for Viability but Collectively Optimize Ribosome Biogenesis and Translation Initiation in Escherichia coliRibosomal RNAs contain numerous conserved nucleotide modifications, yet the functional importance of most of these modifications remains unclear. In Escherichia coli , deletion of individual 16S rRNA ...
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RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS
@aribio.bsky.social

🔬 What we found: ✅ Dual pathways can coexist across diverse archaeal species ✅ Unprecedented structural diversity in bulge-helix-bulge (bhb) motifs, the key elements for circularization. This study reveals remarkable plasticity in archaeal ribosome biogenesis!

doi.orgCircular-pre-rRNA-dependent and -independent rRNA maturation pathways in ArchaeaA monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS
@aribio.bsky.social

🙌 Huge thanks to the amazing team that made this possible: Daniela Strauss, Maximilian Liebl, Pranav Sharma, Michael Jüttner and our collaborators Sarah Berkemer, Aurore Gorlas, and Robert Reichelt for their bioinformatics and biomass support!

doi.orgCircular-pre-rRNA-dependent and -independent rRNA maturation pathways in ArchaeaA monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS
@aribio.bsky.social

But in our new study, we discovered that archaea don’t follow just one script: they can use both circular-dependent and/or circular-independent rRNA maturation pathways! doi.org/10.1261/rna....

doi.orgCircular-pre-rRNA-dependent and -independent rRNA maturation pathways in ArchaeaA monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Beckmann Lab
@beckmannlab.bsky.social

New preprint! 👀RNAse activity has to be tightly regulated.✂️🧬Here, we present the dynamic architecture of the conserved Rixosome complex – a major player in ribosome maturation and heterochromatin maintenance. Our results give insights into its mode of activation.👇 #cryoEM #Ribosome #RNA

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Fabian Blombach
@fblombach.bsky.social

Gene duplication of initiation factor TFIIB drove eukaryotic inventions like the RNA polymerase I, II and III split and probably cyclins. With Kris Kuo and @buzzbaum.bsky.social, we show that the archaeal TFIIB paralogue TFB2 enables a regulated cell cycle in archaea. www.biorxiv.org/content/10.6...

biorxiv.orgA TFIIB paralog drives cyclic transcription to orchestrate the archaeal cell cycleCyclic transcription is a hallmark of the cell cycle. While transcriptional waves in eukaryotes are driven by oscillations in cyclin-dependent kinase (CDK) activity, many archaea have an ordered cell ...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

STCmicrobeblog
@stcmicrobeblog.bsky.social

just a few more #ProtistsOnSky 😊

angela oliverio @oliverio.bsky.social

Just a **few** (aka 25!) more eukaryotic phyla discovered/proposed! www.biorxiv.org/content/10.6... Nice work @tedersoo.bsky.social @vmikk.bsky.social & all

biorxiv.orgDiscovering 25 novel phyla that fill gaps in the eukaryotic tree of lifeProtists play important roles in food chains and symbioses in soil and aquatic environments, displaying an enormous morphological and functional diversity[1][1],[2][2]. While most commonly found proti...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Zeynep Baharoglu
@zeynepbaharoglu.bsky.social

Resistance to antibacterial peptide nucleic acids through altered ribosome function 🦠 www.biorxiv.org/content/10.6...

biorxiv.orgResistance to antibacterial peptide nucleic acids through altered ribosome functionWhen used as antibacterial agents, Peptide Nucleic Acid (PNAs) are generally designed to base-pair with complementary sequences of an essential mRNA and block translation initiation. Although bacteria...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Zeynep Baharoglu
@zeynepbaharoglu.bsky.social

Atlas of stress-induced changes in yeast tRNA modification levels www.biorxiv.org/content/10.6... with a major impact of pH on U34 modification

biorxiv.orgAtlas of stress-induced changes in yeast tRNA modification levelsTransfer RNA (tRNA) modifications are essential for accurate translation and cellular adaptation to environmental changes. Although short-term modification dynamics are well documented, the impact of ...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Florian Mayer
@florianmayer.bsky.social

Excited to share our preprint on Ignicoccus cell divison: only the inner membrane divides, progeny cells accumulate in cell clusters and pop-out! www.biorxiv.org/content/10.6... Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social @tbharat-lab.bsky.social

biorxiv.orgThe life cycle of an archaeon with multiple membranesMany prokaryotes are diderms. They divide using an FtsZ division ring to simultaneously constrict physically coupled inner and outer membranes to form daughter cells with two membranes. Currently, onl...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Molecular Microbiology
@molmicrounihoh.bsky.social

super interesting paper: 👇 Evolutionary Maintenance of Amino Acid Prototrophy in Escherichia coli! academic.oup.com/gbe/article/...

academic.oup.comThe Evolutionary Maintenance of Amino Acid Prototrophy in Escherichia coliAbstract. Escherichia coli is a prototroph and can synthesize all twenty proteinogenic amino acids when required to grow in minimal medium. There are appro

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

DEEMteam_Orsay
@deemteam.bsky.social

Databases may contain lots of misannotated 16S rRNA sequences, which can hinder accurate taxonomic assignment in metabarcoding and metagenomic analyses. We have addressed this issue for Asgard archaea and generated a curated set of high-quality 16S rRNA sequences: academic.oup.com/ismecommun/a...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Beckmann Lab
@beckmannlab.bsky.social

Preprint alert: a helicase watching the ribosomal A-site 👀🧬 Our cryo-EM structure reveals how yeast Dhx29 senses mRNA hairpins forming in the A-site and positions its helicase at the mRNA entry channel to resolve them during translation elongation: doi.org/10.64898/202... #cryoEM #ribosome #RNA

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Jonathan Bohlen
@jonathanbohlen.bsky.social

🧬 New preprint: "Selection and surveillance of 5S ribosomal RNA genes in human populations." The 5S rRNA genes sit in a ~80-copy array on chromosome 1, one of the least-explored parts of the genome. We traced its variation from DNA to ribosome. 1/4🧵

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Nobuto Takeuchi
@nobuto.bsky.social

Sharing our new paper, led by PhD student Daniel Harrison. We propose that archaea aren't pathogenic because those living in eukaryotic hosts lack a metabolic prerequisite, and those with the prerequisite don't live in eukaryotic hosts. #microsky doi.org/10.1128/mbio...

journals.asm.orgWhy are archaea not pathogenic? A hypothesis based on metabolism-habitat covariation | mBioPathogenicity—the ability to cause infectious disease—is widespread among bacteria and eukaryotes but conspicuously absent from archaea, the third domain of life. To understand why archaea are non-pat...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Jamie Cate
@jhdcate.bsky.social

Replying to @jhdcate.bsky.social

And work from the labs of Nicolas Leulliot and Alexandre Smirnov here. 6/ www.biorxiv.org/content/10.6...

biorxiv.orgUniversally conserved isoasparylation sustains ribosome biogenesis and functionAll living beings use ribosomes to synthesize proteins from α-amino acids. Inherited from our common ancestor, a few universally conserved ribosome biogenesis steps, introducing essential ribosomal RN...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Jamie Cate
@jhdcate.bsky.social

Replying to @jhdcate.bsky.social

Congrats to the authors of the two teams who discovered these enzymes! Ours here. 5/ www.biorxiv.org/content/10.6...

biorxiv.orgEnzymatic formation of a conserved isoaspartate in ribosomal protein uS11Isoaspartate (isoAsp) formation is typically viewed as a "molecular clock" through nonenzymatic degradation of aspartate or asparagine during protein aging. Here we report a nearly universal enzymatic...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Mart Krupovic
@mkrupovic.bsky.social

Check out our paper on ESCRTs in large DNA viruses. Most enveloped viruses use the host #ESCRT for envelopment, but only mirusviruses and nucleocytoviricots encode it! Congrats @sonaida.bsky.social, @tomdelmont.bsky.social, Ulysse Guyet & Eugene Koonin. @pasteur.fr www.nature.com/articles/s41...

nature.comLarge eukaryotic DNA viruses encode ESCRT machinery for membrane remodelling - Nature MicrobiologyA genomic screen reveals homologues of ESCRT components in mirusviruses that infect unicellular aquatic eukaryotes.

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Haaris Ahsan Safdari
@haarissafdari.bsky.social

🚨 New in @natcomms.nature.com 🚨 Excited to share our paper on how proline-rich antimicrobial peptides interact with the bacterial ribosome. Using cryo-EM, we found that tiny sequence changes cause these peptides to "flip" orientation in the exit tunnel! 🔄🧫 Read: www.nature.com/articles/s41...

nature.comFlipping antimicrobial peptides in the exit tunnel of the bacterial ribosome - Nature CommunicationsIn this work authors show how minimal mutations in proline-rich antimicrobial peptides can flip their orientation in the ribosome exit tunnel, switching their mechanism from stalling translation termi...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Ákos T Kovács
@evolvedbiofilm.bsky.social

Spatial and genetic constraints govern transcription–translation coupling and mRNA degradation in bacteria -in @natmicrobiol.nature.com www.nature.com/articles/s41...

nature.comSpatial and genetic constraints govern transcription–translation coupling and mRNA degradation in bacteria - Nature MicrobiologyRNase E localization and translation initiation coordinate transcription, translation and mRNA degradation during the life cycle of an mRNA, explaining gene- and species-specific variations in this co...

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Malcolm White
@mfwhite2.bsky.social

gotta love accelerated directed evolution

Nature Microbiology@natmicrobiol.nature.com

Out Now! Bridging classical and continuous directed evolution #MicroSky

go.nature.comBridging classical and continuous directed evolutionNature Microbiology, Published online: 22 May 2026; doi:10.1038/s41564-026-02371-xContinuous evolution methods accelerate directed evolution campaigns, but often at the expense of control over evolutionary outcomes. The lytic selection and evolution system combines the advantages of speed, control and flexibility, adding to recent advances in the directed evolution toolbox.

RNA & Ribosome Homeostasis Lab @École Polytechnique / @CNRS reposted

Maria Barna
@mbarnalab.bsky.social

’m thrilled to share that our paper is out in Molecular Cell! We developed Ribo-Tweezer, a new technology that lets us rapidly and reversibly remove specific proteins from mature ribosomes to ask what they actually do in translation.