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Maria Sokolova

@arimiora.bsky.social
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Lise Meitner Research Group Leader @mpibiochem.bsky.social Bacteriophages

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Reposted by Maria Sokolova
Universität Bayreuth @unibayreuth.bsky.social · 02/07/2026
New Research Unit Funded by the DFG: Investigating the Molecular Machines at the Heart of Gene Expression bit.ly/4oX3h38 #DFG #UniBayreuth #Genetik #Forschungsgruppe #Genexpression
bit.ly
New Research Unit Funded by the DFG: Investigating the Molecular Machines at the Heart of Gene Expression
University of Bayreuth: Our liveable campus university offers innovative, interdisciplinary degree programmes and good career opportunities.
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Reposted by Maria Sokolova
Osterman Ilya @ostermanilya.bsky.social · 09/07/2026
Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️
science.org
Bacteria sense virus-induced genome degradation via methylated mononucleotides
Phages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...
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Reposted by Maria Sokolova
Craig Kaplan @triggerloop.bsky.social · 22/07/2026
Some bacteria use the CRISPR/Cas systems as transcriptional repressors of other anti-phage systems, such that when CRISPR interfered with, gene expression of repressed anti-phage systems goes up www.nature.com/articles/s41...
nature.com
CRISPR–Cas regulates expression of embedded anti-phage defence systems - Nature
CRISPR–Cas systems transcriptionally tune diverse innate defences using CRISPR RNA-like guides to balance antiviral protection with fitness, and hyperactivate these defences when compromised, establis...
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Reposted by Maria Sokolova
Molecular Cell @cp-molcell.bsky.social · 24/05/2026
Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis
dlvr.it
Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis
The roles of water molecules in transcription have long been overlooked due to resolution limitations. Li et al. resolve high-resolution cryo-EM structures of RNA polymerase II and visualize previously undetected water molecules. These waters play essential roles in RNA polymerase II catalysis and in mediating interactions within the transcription machinery.
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Reposted by Maria Sokolova
Molecular Cell @cp-molcell.bsky.social · 25/05/2026
Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity
dlvr.it
Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity
In Mueller et al. the authors capture and visualize the native enzyme-substrate (Michaelis) and product complexes of nucleotide addition by bacterial RNA polymerase. Substrate coordination in a transition-state-like conformation, together with highly coordinated water molecules, suggests a positional (entropic) catalytic mechanism involving specific acid-base chemistry.
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Reposted by Maria Sokolova
Shicheng Guo @shihcheng.bsky.social · 30/05/2026
A study shows DRT4 uses DNA polymerase, exonuclease & RNA endonuclease activities to combat phages. Boosted dNTPs tip balance to polymerization. 🚀 PMID:42166559, Science 2026, @ScienceMagazine doi.org/10.1126/science.aef3178 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
doi.org
https://doi.org/10.1126/science.aef3178
No description available
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Reposted by Maria Sokolova
Miguel López Rivera @riveralopz.bsky.social · 29/05/2026
(1/6) Thrilled to share this story! In our preprint from my PhD in the @kranzuschlab.bsky.social, with help from the Hatfull lab and @soreklab.bsky.social, we discover RyDEP, a phage-encoded RyR-domain glycosidase that allows phages to evade Thoeris defense. Highlights below! doi.org/10.64898/202...
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Reposted by Maria Sokolova
Osterman Ilya @ostermanilya.bsky.social · 30/05/2026
Our aRES story is finally out 😀 Beyond what was reported in the preprint, we found that aRES is activated by direct binding of the phage DNA polymerase. Another NAD-degrading defense system — and multiple phage strategies to overcome it. www.sciencedirect.com/science/arti...
sciencedirect.com
Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases
Many bacterial defense systems restrict phage infection by breaking down the molecule nicotinamide (Nam) adenine dinucleotide (NAD+) into adenosine di…
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Reposted by Maria Sokolova
Sorek Lab @soreklab.bsky.social · 03/06/2026
Our paper is out in Nature Microbiology: functional analysis of 80 phage sponges, revealing new sponges that inhibit bac immunity by binding the immune signals cCMP, cUMP and N7-cADPR Thanks to all coauthors and our collaborators at the Kranzusch Lab. Congrats Romi! www.nature.com/articles/s41...
nature.com
Functional diversity of phage sponge proteins that sequester host immune signals - Nature Microbiology
A functional screen reveals phage sponge proteins that bind Pycsar, Thoeris and CBASS signalling molecules to inhibit bacterial immunity.
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Reposted by Maria Sokolova
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 06/06/2026
Balancing of immune activation and suppression during phage infection www.biorxiv.org/content/10.64898/20…
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Reposted by Maria Sokolova
Christine Mayr @christinemayr.bsky.social · 08/06/2026
Finally out in @Cellcellpress! Proteins with long IDRs are prone to misfolding during protein synthesis. This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones. www.cell.com/cell/fulltex...
cell.com
mRNA 3′ UTRs chaperone intrinsically disordered regions to control protein activity
Highly conserved mRNA 3′ UTRs act as co-translational chaperones for intrinsically disordered regions (IDRs), preventing inter-domain misfolding and enabling biogenesis of fully active proteins.
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Reposted by Maria Sokolova
Rafal Mostowy @rafalmostowy.bsky.social · 10/06/2026
Phage receptor-binding proteins are known for their LEGO-like modularity, but we still do not fully understand their evolutionary potential and how it shapes phage host range. Our new preprint examines this systematically in Klebsiella phages. 🔗 www.biorxiv.org/content/10.6... Thread 🧵
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Reposted by Maria Sokolova
The EMBO Journal @embojournal.org · 10/06/2026
CapK is a bacterial DNA damage-activated kinase that phosphorylates transcriptional repressor CapS to control adjacently-encoded anti-phage immune pathway genes in response to a universal stress signal, DNA damage @kevincorbett.bsky.social and colleagues link.springer.com/article/10.1...
link.springer.com
A DNA damage-activated kinase phosphorylates a transcriptional repressor to control bacterial immune pathway expression - The EMBO Journal
Bacteria encode numerous stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune ...
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Reposted by Maria Sokolova
EMBL-EBI @ebi.embl.org · 28/05/2026
We told you it wouldn’t be a long wait. 👀 Even more predicted protein structures have been added to the #AlphaFold Database. This time, the database has expanded to include heterodimers – protein complexes made up of two different proteins. alphafold.ebi.ac.uk
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Reposted by Maria Sokolova
Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 19/05/2026
Predicting phage anti-defenses that shoot the messenger Mahler & @yuping-li.bsky.social highlight @science.org work developing a structure-guided approach to identify phage proteins counteracting bacterial nucleotide signaling defenses using metagenomic data. www.cell.com/cell-host-mi...
cell.com
Predicting phage anti-defenses that shoot the messenger
Locked in a constant arms race, bacteria and their phage predators have evolved various defenses and counter-defenses. Compared to the numerous identified defenses, phage-encoded counter-defenses are ...
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Reposted by Maria Sokolova
Sternberg Lab @sternberglab.bsky.social · 21/05/2026
1/8 🚨 New preprint from the @sternberglab.bsky.social & @martinjinek.bsky.social labs! CRISPR-associated transposases (CASTs) insert large DNA cargoes at precise genomic locations — no double-strand breaks needed.
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Reposted by Maria Sokolova
Aude Bernheim @audeber.bsky.social · 22/05/2026
Great piece and cover @science.org about how our field is uncovering the evolutionary and mechanistic connections between bacterial and eukaryotic immunity ! www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
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Max-Planck-Gesellschaft @maxplanck.de · 21/05/2026
Don’t like #networking? Don’t give up too quickly! Even a casual chat with colleagues can be a first step. 🤗 A guide for researchers who tend to panic when they’re at a loss for words. www.nature.com/articles/d41... @nature.com #ScienceCareer
nature.com
A step-by-step guide for scientists who hate conference networking
If the thought of ‘working’ a room packed with strangers fills you with dread, academic careers coach Caroline Dunne has some advice.
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Reposted by Maria Sokolova
Vivek Mutalik @vivekmutalik.bsky.social · 20/05/2026
🎊 New Preprint from phagefoundry.org ! Super excited to share our latest work on generating systematic phage-MDR P. aeruginosa interaction dataset & use of ML to predict phage susceptibility & phage cocktails from target genome sequences alone, w validations www.biorxiv.org/cgi/content/...
Systematic lytic host range characterization of 99 multidrug resistant Pseudomonas aeruginosa strains against 95 diverse double strand DNA phages, and AI/ML workflow to predict phage susceptibility and cocktail formulation based on genomic sequence alone.
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Reposted by Maria Sokolova
Jakob T Rostøl @jakob-tr.bsky.social · 20/05/2026
Like a prophage being awakened from its slumber, the phage field has seen a lot of renewed activity during the last decade. Check out our new @natrevmicro.nature.com review on the temperate phage life cycle here to stay up-to-date 🧫🦠 www.nature.com/articles/s41...
nature.com
Revisiting the life cycle of temperate phages - Nature Reviews Microbiology
The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...
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Reposted by Maria Sokolova
Emmanuele Severi @emmseveri.bsky.social · 13/04/2026
#microsky #phagesky Jumbo #phage PhiKZ www.nature.com/articles/s41...
nature.com
Structural atlas of the intact jumbo phage phiKZ - Nature Communications
Jumbo phages are bacterial viruses with large genomes, oversized icosahedral capsids and complex tail architectures. Here, the authors use cryo-EM to provide a detailed structural analysis of jumbo ph...
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Reposted by Maria Sokolova
Molecular Cell @cp-molcell.bsky.social · 30/04/2026
Online Now: Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity Online now:
dlvr.it
Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity
In Mueller et al. the authors capture and visualize the native enzyme-substrate (Michaelis) and product complexes of nucleotide addition by bacterial RNA polymerase. Substrate coordination in a transition-state-like conformation, together with highly coordinated water molecules, suggests a positional (entropic) catalytic mechanism involving specific acid-base chemistry.
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Reposted by Maria Sokolova
Molecular Cell @cp-molcell.bsky.social · 01/05/2026
Online Now: Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis Online now:
dlvr.it
Sub-2 Å cryo-EM structures of transcribing RNA polymerase II reveal critical roles of water molecules in catalysis
The roles of water molecules in transcription have long been overlooked due to resolution limitations. Li et al. resolve high-resolution cryo-EM structures of RNA polymerase II and visualize previously undetected water molecules. These waters play essential roles in RNA polymerase II catalysis and in mediating interactions within the transcription machinery.
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Reposted by Maria Sokolova
Julia Frunzke @frunzkelab.bsky.social · 06/05/2026
Very happy to share our recent preprint: “An Lsr2-like xenogeneic silencer confers immunity against AT-rich bacteriophage infection” www.researchsquare.com/article/rs-9... @fz-juelich.de; @hhu.de; @spp2330.bsky.social
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Reposted by Maria Sokolova
Mart Krupovic @mkrupovic.bsky.social · 11/05/2026
With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...
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Reposted by Maria Sokolova
Sternberg Lab @sternberglab.bsky.social · 12/05/2026
1/9 New preprint from the Sternberg Lab in collaboration with the Nishimasu Lab! We uncover how the DRT3 antiphage immune system pairs two reverse transcriptases, one RNA-templated and one protein-templated, to build a double-stranded DNA effector. doi.org/10.64898/202...
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Reposted by Maria Sokolova
Luuk Loeff @lloeff.bsky.social · 14/05/2026
Together, our data support a model in which DruH processes replication-associated forked DNA structures to generate 5′ overhangs that trigger activation of the autoinhibited helicase–nuclease DruE, enabling selective DNA degradation during phage defense.
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Reposted by Maria Sokolova
Sternberg Lab @sternberglab.bsky.social · 04/03/2026
Out now! In collaboration with Leifu Chang, we uncover the molecular and structural underpinnings of CRISPR-Cas12f-like RNA-guided transcription systems! Links to the published articles: tinyurl.com/55kpavet tinyurl.com/sk6djwx3 Previous thread for the preprint: bsky.app/profile/did:...
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Reposted by Maria Sokolova
Aritz Roa-Eguiara @aritz-roa.bsky.social · 07/03/2026
🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process. www.biorxiv.org/content/10.6...
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Aude Bernheim @audeber.bsky.social · 02/04/2026
How diverse is bacterial immunity ? We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems. 👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie... Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
science.org
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Reposted by Maria Sokolova
Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Reposted by Maria Sokolova
Peter DeWeirdt @pdeweirdt.bsky.social · 02/04/2026
Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...
science.org
DefensePredictor: A machine learning model to discover prokaryotic immune systems
Antiphage defense systems protect bacteria from viral infection and have inspired important biotechnologies such as CRISPR-Cas9 while also revealing the evolutionary roots of eukaryotic innate immunit...
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Reposted by Maria Sokolova
Kenneth Loi @kenjmloi.bsky.social · 27/04/2026
Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.
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Tera Levin @teralevin.bsky.social · 02/05/2026
Bacterial immune proteins have repeatedly evolved to become parts of eukaryotic immunity. But how? Our new preprint uncovers a recent horizontal transfer event & shows how eukaryotes co-opted a toxic bacterial immune protein 🦠🧪🧵 1/
Microscopy image showing yeast cells expressing a fluorescently tagged version of the amoeba TirC protein. TirC forms filaments that span the yeast cells.
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Reposted by Maria Sokolova
Joe Bondy-Denomy @jbdsf.bsky.social · 06/01/2026
Wow!
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 30/01/2026
Chemical inhibition of a bacterial immune system Small molecules inhibit type II Thoeris anti-phage systems from diverse bacteria. One compound, IP6C, improves phage-therapy against P. aeruginosa & is effective against Thoeris in polymicrobial communities www.cell.com/cell-host-mi...
cell.com
Chemical inhibition of a bacterial immune system
Bacteriophages are promising alternatives to antibiotics for treating bacterial infections. However, bacteria possess immune systems that neutralize bacteriophages. Zang et al. discover small molecule...
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Reposted by Maria Sokolova
Kranzusch Lab @kranzuschlab.bsky.social · 06/02/2026
Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity! www.nature.com/articles/s41...
nature.com
The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology
The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...
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Current Research in Microbial Sciences @microbesinfect.bsky.social · 07/02/2026
Molecular basis for anti-jumbo phage #immunity by AVAST type 5. Avs5 detects an early jumbo‑phage activator and halts infection by rapidly hydrolyzing NAD+. www.sciencedirect.com/science/arti... #phage #bacteriophage #MicroSky
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Alexander Harms @aharms485.bsky.social · 20/11/2025
🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8
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Joe Bondy-Denomy @jbdsf.bsky.social · 08/12/2025
Phages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out tinyurl.com/bdcfrejh
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Julia Frunzke @frunzkelab.bsky.social · 14/01/2026
Save the date, please RT: Looking forward to an exciting International Symposium @spp2330.bsky.social "New concepts in prokaryotic virus-host interactions". October 5-7, 2026; Harnack-Haus Berlin (Germany). @dfg.de @hhu.de @fz-juelich.de
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Reposted by Maria Sokolova
Sternberg Lab @sternberglab.bsky.social · 17/10/2025
1/10 Genome maintenance by telomerase is a fundamental process in nearly all eukaryotes. But where does it come from? Today, we report the discovery of telomerase homologs in a family of antiviral RTs, revealing an unexpected evolutionary origin in bacteria. www.biorxiv.org/content/10.1...
biorxiv.org
Antiviral reverse transcriptases reveal the evolutionary origin of telomerase
Defense-associated reverse transcriptases (DRTs) employ diverse and distinctive mechanisms of cDNA synthesis to protect bacteria against viral infection. However, much of DRT family diversity remains ...
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Reposted by Maria Sokolova
Sternberg Lab @sternberglab.bsky.social · 14/11/2025
1/9 Metagenomics lets us read microbiomes in nature without cultivation, but writing (editing) them in their native context is still a major challenge. Meet MetaEdit: a platform for pathway-scale metagenomic editing inside the gut microbiome. science.org/doi/10.1126/...
science.org
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
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Reposted by Maria Sokolova
Stephan Gruber @gruberlab.bsky.social · 09/10/2025
How do SMC complexes load onto DNA to get ready for loop extrusion? @roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️. Check out the new paper: www.cell.com/molecular-ce...
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Sorek Lab @soreklab.bsky.social · 18/10/2025
NAD+ is a central molecule in bacterial immunity. An excellent and timely review by Hugo Vausset and Aude Bernheim
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Seth Shipman @seth-shipman.bsky.social · 23/10/2025
Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1... Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.
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Nature Microbiology @natmicrobiol.nature.com · 24/10/2025
New article alert: Bacterial TIR-based immune systems sense phage capsids to initiate defense Out now in Nature Microbiology by Cameron G. Roberts, Chloe B. Fishman, Zhiying Zhang, Dalton V. Banh, Dinshaw J. Patel & Luciano A. Marraffini #microsky www.nature.com/articles/s41...
nature.com
Bacterial TIR-based immune systems sense phage capsids to initiate defense - Nature Microbiology
After sensing capsids, the Thoeris antiphage defense system triggers a cascade that leads to NAD+ cleavage and cell arrest, which are dynamics that are mirrored in some mammalian immune pathways.
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Reposted by Maria Sokolova
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 03/11/2025
A membrane-bound nuclease directly cleaves phage DNA during genome injection www.biorxiv.org/content/10.1101/202…
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Reposted by Maria Sokolova
Osterman Ilya @ostermanilya.bsky.social · 06/11/2025
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides. Here’s the story of how we discovered the Metis defense system 👇 www.biorxiv.org/content/10.1...
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Osterman Ilya @ostermanilya.bsky.social · 14/11/2025
Fascinating discovery - anti-phage defense protein is a proenzyme that is cleaved by partner protease after phage infection and all three! products of cleavage form active nuclease.
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