Wilson Lab

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  Alexey Amunts handle.invalid · 19h
  We're launching a research lab at SMART. Shenzhen Medical Academy for Research and Translation is a newly established institute with long-term funding mechanisms for internal and external investigators. At full capacity SMART aims to support up to 400 labs. www.scmp.com/news/china/s...
  

  Structural biologist Alexey Amunts launches new research lab in Shenzhen

  ‘Shenzhen adds another dimension; it is a place where ideas do not remain ideas for long,’ Amunts says of new position.

  scmp.com
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  Marie Winz mariewinz.bsky.social · Feb 1
  Replying to Marie Winz
  4 - Still lots to learn about this mysterious factor. 🔗 Read the paper: academic.oup.com/nar/article/... Funded by @dfg.de via SFB TRR319-RMaP 🙏 #RibosomeBiology #TranslationQC #RNA #Nanopore #Yeast #PhDPosition #DFG #RMaP #New1
  

  Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay

  Abstract. New1 is a homologue of the essential yeast translation elongation factor eEF3. Lack of New1 has been shown to induce ribosome queuing upstream of

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  Marie Winz mariewinz.bsky.social · Feb 1
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  Osterman Ilya handle.invalid · Jan 29
  🧬 Metabolic arms race continues! We discovered a new NAD⁺-depleting bacterial immune system aRES and phage enzymes that overcome it. Our preprint is out: www.biorxiv.org/content/10.6...

  Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases

  Many bacterial defense systems restrict phage infection by breaking the molecule NAD+ to its constituents, adenosine diphosphate ribose (ADPR) and nicotinamide (Nam). To counter NAD+ depletion-mediated defense, phages evolved NAD+ reconstitution pathway 1 (NARP1), which uses ADPR and Nam to rebuild NAD+. Here we report a bacterial defense system called aRES, involving RES-domain proteins that degrade NAD+ into Nam and ADPR-1″-phosphate (ADPR-1P). This molecule cannot serve as a substrate for NARP1, so that NAD+ depletion by aRES defends against phages even if they encode NARP1. We further discover that some phages evolved an extended NARP1 pathway capable of overcoming aRES defense. In these phages, the NARP1 operon also includes a specialized phosphatase, which dephosphorylates ADPR-1P to form ADPR, a substrate from which NARP1 then reconstitutes NAD+. Other phages encode inhibitors that directly bind aRES proteins and physically block their active sites. Our study describes new layers in the NAD+-centric arms race between bacteria and phages and highlights the centrality of the NAD+ pool in cellular battles between viruses and their hosts. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, ERC-AdG GA 101018520 Israel Science Foundation, MAPATS grant 2720/22 Deutsche Forschungsgemeinschaft, SPP 2330, grant 464312965 Minerva Foundation with funding from the Federal German Ministry for Education and Research research grant from Magnus Konow in honor of his mother Olga Konow Rappaport Ministry of Aliyah and Immigrant Absorption, https://ror.org/05aycsg86 Clore Scholars Program

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  Haselbach Lab haselbachlab.bsky.social · Jan 19
  Have a look at our new structure of co translational folding in yeast. This is collaborative work initialized by the Rospert lab from the @uni-freiburg.de. Structural work has been done by the amazing @lgrundmann.bsky.social Stay tuned for the next ribosome paper from him, following very soon.
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    IMP impvienna.bsky.social · Jan 19
    🧪Scientists from our Haselbach lab captured how proteins begin to fold as they’re being made. Using cryo-EM, they visualised chaperones guiding nascent proteins on the ribosome: nature.com/articles/s41467-025…
    
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  Sorek Lab soreklab.bsky.social · Jan 29
  We found a new mode by which bacteria deplete NAD+ to protect from phages. And then we found how phages overcome this defense Discovered by talented biochemist Dr Ilya Osterman, read the preprint: tinyurl.com/Narp-ap A thread 🧵

  Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases

  Many bacterial defense systems restrict phage infection by breaking the molecule NAD+ to its constituents, adenosine diphosphate ribose (ADPR) and nicotinamide (Nam). To counter NAD+ depletion-mediated defense, phages evolved NAD+ reconstitution pathway 1 (NARP1), which uses ADPR and Nam to rebuild NAD+. Here we report a bacterial defense system called aRES, involving RES-domain proteins that degrade NAD+ into Nam and ADPR-1″-phosphate (ADPR-1P). This molecule cannot serve as a substrate for NARP1, so that NAD+ depletion by aRES defends against phages even if they encode NARP1. We further discover that some phages evolved an extended NARP1 pathway capable of overcoming aRES defense. In these phages, the NARP1 operon also includes a specialized phosphatase, which dephosphorylates ADPR-1P to form ADPR, a substrate from which NARP1 then reconstitutes NAD+. Other phages encode inhibitors that directly bind aRES proteins and physically block their active sites. Our study describes new layers in the NAD+-centric arms race between bacteria and phages and highlights the centrality of the NAD+ pool in cellular battles between viruses and their hosts. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, ERC-AdG GA 101018520 Israel Science Foundation, MAPATS grant 2720/22 Deutsche Forschungsgemeinschaft, SPP 2330, grant 464312965 Minerva Foundation with funding from the Federal German Ministry for Education and Research research grant from Magnus Konow in honor of his mother Olga Konow Rappaport Ministry of Aliyah and Immigrant Absorption, https://ror.org/05aycsg86 Clore Scholars Program

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  Molecular Cell cp-molcell.bsky.social · Jan 28
  Online Now: Signaling to make human ribosomes: Connections between the cytoplasm and the nucleolus Online now:
  

  Signaling to make human ribosomes: Connections between the cytoplasm and the nucleolus

  Lawrence et al. examine how ribosome production in the eukaryotic nucleolus is coordinated by cytoplasmic processes to maintain appropriate ribosome numbers. The authors highlight regulatory inputs from cytoplasmic signaling, mitosis, and cytoplasmic organelles that converge on nucleolar function, and they discuss how disruption of these pathways contributes to human disease.

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  Joachim Frank joachim123.bsky.social · Jan 29
  now online: academic.oup.com/nar/article/...
  

  Structures of naked mole-rat, tuco-tuco, and guinea pig ribosomes—is rRNA fragmentation linked to translational fidelity?

  Abstract. Ribosomes are central to protein synthesis in all organisms. In mammals, the ribosome functional core is highly conserved. Remarkably, two rodent

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  IgnatovaLab ignatovalab.bsky.social · Jan 27
  Interested in direct tRNA-seq by Nanopore? We developed a new RNA-based barcoding aproach for seq parallelization; it is also cost-saving. Scripts available on github. #tRNA #Nanopore track.smtpsendmail.com/9032119/c?p=...
  

  ADAM-tRNA-seq: an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing

  Abstract. Transfer RNAs (tRNAs) play an essential role in protein synthesis and cellular homeostasis, and their dysregulation is associated with various hu

  track.smtpsendmail.com
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  bioRxiv Cell Biology handle.invalid · Jan 27
  Active transport of tRNAs facilitates distributed protein synthesis biorxiv.org/content/10.64898/20…
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  Structura Biotechnology handle.invalid · Jan 27
  🚀 CryoSPARC v5.0 BETA is here! We’re excited to deploy another major #CryoSPARC release to help enable and accelerate #cryoEM data analysis. v5 has a redesigned underlying software system and many new features - highlights in thread! Full changelog: cryosparc.com/updates/v5.0.0
  
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  Molecular Cell cp-molcell.bsky.social · Jan 28
  Online Now: Why m⁶A? An RNA surveillance model Online now:
  

  Why m⁶A? An RNA surveillance model

  Dierks and Schwartz discuss the m6A surveillance model, proposing that m6A flags “undesirable” intron-less RNAs (e.g., transposons) for decay. This provides a mechanism to distinguish “legitimate” spliced mRNAs and potentially suppress harmful RNA.

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  Zeynep Baharoglu zeynepbaharoglu.bsky.social · Jan 26
  Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation #rnasky 🦠
  

  Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation - Nature Communications

  Small regulatory RNAs can act on target mRNAs to control their translation and stability. Here, the authors present evidence that this riboregulation can potentially regulate by pairing to a target si...

  nature.com
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  Kurianlab kurianlab.bsky.social · Jan 24
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  Matthew Bowler handle.invalid · Jan 22
  New Preprint alert! Excited to share our latest work on the #MAPKinases from stellar PhD student Jill von Velsen. First structures of the MAP2K MEK1 activating its substrate MAPK between 2.9 and 3.6A - amazing resolutions for such a small and mobile complex! www.biorxiv.org/content/10.6...
  
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  Haselbach Lab haselbachlab.bsky.social · Jan 22
  And the 4th paper in this week contribution from our lab tells about ribosome biogenesis in yeast. A follow-up story from our wonderful collaborators in Graz - the Bergler Lab. Structural work was again done by the amazing @lgrundmann.bsky.social: academic.oup.com/nar/article/...
  

  A comprehensive view on r-protein binding and rRNA domain structuring during early eukaryotic ribosome formation

  Abstract. Formation of the eukaryotic ribosomal subunits follows a strict regime to assemble ribosomal proteins (r-protein) with ribosomal RNAs (rRNA) whil

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  IMP impvienna.bsky.social · Jan 19
  🧪Scientists from our Haselbach lab captured how proteins begin to fold as they’re being made. Using cryo-EM, they visualised chaperones guiding nascent proteins on the ribosome: nature.com/articles/s41467-025…
  
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  Innis Lab handle.invalid · Jan 17
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  Waggoner Lab labwaggoner.bsky.social · Jan 15
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  Shicheng Guo handle.invalid · Jan 11
  Ribosome collisions activate ZAK, influencing cell fate via p38 & JNK phosphorylation. Biochemistry & cryo-EM uncover distinct ZAK-ribosome interactions. PMID:41261136, Nature 2025, @Nature doi.org/10.1038/s41586-025-… #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
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  Alexey Amunts handle.invalid · Jan 10
  Only in Shenzhen: Science Nature coffee bar. If you’ve published in @science.org or @nature.com, they give you coffee for free. 100% real!
  
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  Ruben Gonzalez handle.invalid · Jan 5
  Slightly overdue article highlight! In PNAS, we use smFRET to reveal how polypeptide release factor 2 (RF2) undergoes a cascade of structural changes to catalyze polypeptide release during translation termination and ArfA-mediated ribosome rescue. 🧵⬇️ doi.org/10.1073/pnas...
  
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  Tomek Wlodarski twlodarski.bsky.social · Dec 30, 2025
  Just in time for 2026! 🎆 Presenting a nascent-centric view on the shape of the ribosomal exit tunnel topology, based on MD-derived occupancy maps for 55 distinct ribosomes. 🧶🧬🖥️ 📄 Read the preprint: biorxiv.org/content/10.6... #StructuralBiology #Ribosome #CryoEM #Evolution #Biophysics
  

  Evolution of the ribosomal exit tunnel through the eyes of the nascent chain

  The ribosomal exit tunnel is a universally conserved feature of the large subunit that directs the nascent polypeptide chain into the cellular environment and is involved in co-translational folding, ...

  biorxiv.org
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  Jennifer Cash jencash.bsky.social · Dec 30, 2025
  Interested in learning or strengthening skills in #CryoEM single particle analysis? Apply for the CSHL cryo-EM course happening in March! This is a super intense 2 week course covering theory up through data deposition. Apps due Jan 9! Info here: meetings.cshl.edu/courses.aspx...
  

  Cryo-Electron Microscopy

  Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.

  meetings.cshl.edu
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  Heather Feaga heatherfeaga.bsky.social · Dec 25, 2025
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  Boël Lab boellab.bsky.social · Dec 23, 2025
  In this study, we highlight the importance of the base composition of the first codons for protein expression. An increased abundance of adenine (A) and a decrease in guanine (G) enhance expression and improve mRNA stability. The mediator of this effect is the ribosome.
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    Boël Lab boellab.bsky.social · Dec 23, 2025
    Our latest paper on protein expression and mRNA stability is out! academic.oup.com/nar/article/... Check out how to increase your protein output with a simple trick. Congratulations to first author @Anna Lipońska, it was a great collaboration with the Aalberts group. #RNAsky #ribosome #EGM
    

    Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli

    Abstract. Protein synthesis efficiency is highly dependent on the messenger RNA (mRNA) coding sequence. Furthermore, there is extensive evidence of a corre

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  Hanjin Liu liu-hanjin.bsky.social · Dec 23, 2025
  CryoEM folks, If you want to handle huge STAR file efficiently in Python, please try starfile-rs! github.com/hanjinliu/star… Reading a motion data of a particle from a 15 MB file is just like this ↓🤩
  
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  Michael Hothorn handle.invalid · Dec 24, 2025
  A 1.25 A!!! cryo EM structure of rubisco.
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    cryoEM papers cryoempapers.bsky.social · Dec 24, 2025
    Atomic resolution structure of spinach rubisco reveals protons and dynamics www.biorxiv.org/content/10.64898/2025.12.22.696010v1 #cryoEM
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  Heather Feaga heatherfeaga.bsky.social · Dec 20, 2025
  www.biorxiv.org/content/10.6...
  

  Structural Basis of TACO1-Mediated Efficient Mitochondrial Translation

  Translation elongation is a universally conserved step in protein synthesis, relying on elongation factors that engage the ribosomal L7/L12 stalk to mediate aminoacyl-tRNA delivery, accommodation, and...

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  The BanLab thebanlab.bsky.social · Dec 20, 2025
  Last X-Mas, the ribosome gave you methionine, but the very next day, MetAP took it away. This year, to save histones from tears, NatD gives you an acetyl group. ⭐️ Explore our latest paper with the Deuerling lab @uni-konstanz.de and Shu-ou Chan lab @caltech.edu! www.science.org/doi/10.1126/...
  

  Mechanism of cotranslational modification of histones H2A and H4 by MetAP1 and NatD

  NAC enables cotranslational N-terminal processing of histones H2A and H4 by recruiting MetAP1 and NatD at the ribosomal tunnel.

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  Oli Clarke handle.invalid · Dec 18, 2025
  very unusual - a tRNA regulated anion channel
  
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    cryoEM papers cryoempapers.bsky.social · Dec 18, 2025
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  Wilson Lab wilsonlab.bsky.social · Dec 18, 2025
  www.rnatherapeutics.org
  

  RNA Therapeutics Hybrid Conference

  RNATx symposium brings together attendees from around the globe and across the full spectrum of RNA therapeutics offering access to innovative research, networking opportunities, and the latest techno...

  rnatherapeutics.org
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  Wilson Lab wilsonlab.bsky.social · Dec 14, 2025
  www.nature.com/articles/s41...
  

  AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination - Nature Methods

  An analysis of AlphaFold protein structure predictions shows that while in many cases the predictions are highly accurate, there are also many instances where the predicted structures or parts of pred...

  nature.com
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  Anthony Vecchiarelli handle.invalid · Dec 12, 2025
  Just got word that we are a go for the Bacterial Cell Biology and Development GRS and GRC at Southern New Hampshire University! GRS will be on June 5-6, 2027 GRC will be from June 6-11, 2027 Block off your calendars Prokaryotic Cell Biologists! More details to come! Please repost!
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  Frances Yap ribo1214.bsky.social · Dec 10, 2025
  🔽 !!??? #RNASky 🧪
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    bioRxivpreprint handle.invalid · Dec 9, 2025
    3' to 5' Translation of Circular RNAs? biorxiv.org/content/10.64898/20…
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  Molecular Cell cp-molcell.bsky.social · Dec 10, 2025
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  Ruben Gonzalez handle.invalid · Dec 10, 2025
  The Gonzalez Lab at Columbia University is seeking a scientific leader! Join us in a Research Scientist position, driving single-molecule, structural, and biochemical studies of translation, translational control, and other RNA-based processes. Apply: apply.interfolio.com/176949
  
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  Wilson Lab wilsonlab.bsky.social · Dec 9, 2025
  pubmed.ncbi.nlm.nih.gov/41341057/
  

  Hybrid Antibiotics Targeting the Bacterial Ribosome - PubMed

  Antimicrobial resistance remains a formidable challenge to modern medicine, with bacterial resistance mechanisms increasingly eroding the utility of clinically important antibiotics. While recent efforts have expanded the antibacterial pipeline, the development of resistance in priority pathogens co …

  pubmed.ncbi.nlm.nih.gov
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  IBMP | Institut de biologie moléculaire des plantes ibmp-cnrs.bsky.social · Dec 3, 2025
  How plant mitochondria make their own proteins 🌱🔬 A new study published in @natcomms.nature.com reveals the structure of the cauliflower mitoribosome and a unique RsgA mechanism that blocks premature translation. ▶️https://nature.com/articles/s41467-025-65864-z #PlantBiology #CryoEM #Ribosome
  
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  Korostelev Lab korostelevlab.bsky.social · Dec 5, 2025
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  Simon Bekker-Jensen lab bekkerjensenlab.bsky.social · Dec 3, 2025
  New preprint out! Our latest work on how ZAKα is activated by stalled or/and collided ribosomes is now online🎉. #Ribosome #RibotoxicStressResponse #ZAKα #Translation #mRNA www.biorxiv.org/content/10.1...
  

  ZAKα is a sensor of mRNA stasis at the ribosomal exit channel

  Despite a growing interest in the ribotoxic stress response (RSR), it remains unknown how the upstream p38 and JNK-activating MAP3 kinase ZAKα senses translational impairment. Combining Alphafold3 pre...

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  Martin Ott lab mitolab.bsky.social · Dec 3, 2025
  Our study on the molecular function of translational activators for mitochondrial protein synthesis is published: rdcu.be/eSWxT A great collaboration with @stirlingchurchman.bsky.social and @sshaolab.bsky.social with structural work from our @pelleeas.bsky.social Funded by @kawresearch.bsky.social
  

  Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation

  Nature Structural & Molecular Biology - Mitochondrial translational activators (TAs) facilitate transcript-specific translation. Using selective ribosome profiling and cryo-electron microscopy,...

  rdcu.be
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  Nikolai Slavov slavov-n.bsky.social · Nov 30, 2025
  The epitranscriptome formed by the growing number of modifications occurring within mRNA transcripts. We have been mapping mRNA modifications for over a decade. => Characterizing their functions -- especially on translation -- is a research frontier.
  
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  Wilson Lab wilsonlab.bsky.social · Dec 1, 2025
  pubmed.ncbi.nlm.nih.gov/41282059/
  

  Saskemycin, a potent and selective antimycobacterial agent targeting a unique site on the ribosome - PubMed

  Tuberculosis is the deadliest bacterial disease on the planet. The months-long regimen of multiple antibiotics required to treat tuberculosis profoundly affects the microbiome and leads to the development of antimicrobial resistance. Furthermore, non-tuberculous mycobacterial infections pose an incr …

  pubmed.ncbi.nlm.nih.gov
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  Korostelev Lab korostelevlab.bsky.social · Nov 30, 2025
  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...
  
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  Hopfner Lab handle.invalid · Nov 27, 2025
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  Frances Yap ribo1214.bsky.social · Nov 26, 2025
  #Ribosome #hibernation 🧪
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    bioRxiv Microbiology biorxiv-microbiol.bsky.social · Nov 26, 2025
    Structure of the Hibernating Francisella tularensis Ribosome and Mechanistic Insights into Its Inhibition by Antibiotics biorxiv.org/content/10.1101/202…
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  Jeremy Berg handle.invalid · Nov 24, 2025
  My quote of the day For every complex problem there is an answer that is clear, simple, and wrong. H. L. Mencken
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  Gene Center Munich @LMU Munich genecenter-lmu.bsky.social · Nov 25, 2025
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  greenlab greenlab.bsky.social · Nov 24, 2025
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  Tominaga K. (tomiken) pacyc184.bsky.social · Nov 24, 2025
  Evolutionary Flexibility of Ribosome Biogenesis in Bacteria | Molecular Biology and Evolution | Oxford Academic academic.oup.com/mbe/article/42/11/m…
  

  Evolutionary Flexibility of Ribosome Biogenesis in Bacteria

  Abstract. Ribosomes are essential for protein synthesis and require ribosome biogenesis factors for assembly. To uncover the evolutionary diversity of ribo

  dx.doi.org
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  Beckmann Lab beckmannlab.bsky.social · Nov 23, 2025
  How does the kinase ZAK sense ribosome collisions? Find out in our latest collaboration with the @greenlab.bsky.social @doubleshuang.bsky.social @Vienna Huso: 1/4 rdcu.be/eRmJl #ribosome #cryoEM #LMU #JHMI
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  Beckmann Lab beckmannlab.bsky.social · Nov 23, 2025
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  Susan Schlimpert handle.invalid · Nov 20, 2025
  Bacteriologists - save the date for the next BacNet meeting in September 2026 #BacNet26 organised by @lalouxlab.bsky.social
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    Ákos T Kovács handle.invalid · Nov 20, 2025
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