artemisaev
Everything phage biology and bacterial immunity
Assistant professor at Skoltech, Russia
- Reposted by artemisaevWe 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 🧵
- Reposted by artemisaevPreprint out: We characterise PUA-Cal-HAD, a widespread bacterial antiphage defence family. An infection cue switches a preassembled complex into an immune filament that drains dNTPs via a coupled two-enzyme cascade, and phage DNA mimics can block filament assembly (anti-polymerisation).
- Reposted by artemisaevMost plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social
- Reposted by artemisaevOur paper is out! Hiding in plain sight among Cas12a nucleases, Cas12a3 cleaves not its RNA target but the 3′ ends of tRNA. Huge thanks to all who made this possible, especially the Beisel lab, Biao & Dirk for the structure, & @sebastianglatt.bsky.social for all things tRNA. doi.org/10.1038/s415...
- Reposted by artemisaevThe EMBO Gold Medal 2025 was awarded to Tanmay Bharat and David Bikard: embo.org/press-releases/embo… 🧪 At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
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- Reposted by artemisaevOnline Now: The Ppl protein senses 3′-hydroxyl DNA overhangs and NTP depletion to halt phage infection Online now:
- Reposted by artemisaevwww.nature.com/articles/s41... Structural mechanism of the Retron-Eco7 anti-phage defense system
- Reposted by artemisaev⭐ NAR Breakthrough! ⭐ 🦠 New study shows phage X1 hijacks Yersinia's enterocolitica flagellum to inject its DNA directly into the cytosol. Yersinia, though, strikes back! 🦠 A fascinating look at the #dualrole of #flagella in #viralentry and #bacterialimmunity. 🧬 Read more: doi.org/10.1093/nar/...
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- Reposted by artemisaev🚨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
- Reposted by artemisaevFirst the link to the preprint: www.biorxiv.org/content/10.1...
- Reposted by artemisaevI’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.
- Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses biorxiv.org/content/10.1101/202…
- Reposted by artemisaevSurviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses biorxiv.org/content/10.1101/202…
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- Reposted by artemisaev🚨vConTACT3 preprint live!🚨(Peer Review soon...!) vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification. 🔗 Read the preprint: doi.org/10.1101/2025... Improvements details below 👇
- Reposted by artemisaevBacteria 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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- Reposted by artemisaevI’m thrilled to share our Retron Eco8 paper published in Molecular Cell today. Thanks all Fu lab members and our collaborators. 👉Phage SSB detection by retron Eco8 msDNA unleashes nuclease-mediated immunity. www.cell.com/molecular-ce...
- Reposted by artemisaevBeen 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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- Reposted by artemisaevHappy that the final version of our Lamassu work @yli18smc.bsky.social is now out: www.nature.com/articles/s41... Thanks again to our awesome collaborators @mblokesch.bsky.social and David and co and Mark Szczelkun and @steven-shaw.bsky.social and the DCI Lausanne @fbm-unil.bsky.social
- Glad to share the work of @yli18smc.bsky.social and co on Lamassu, a bacterial defense system related to Rad50/Mre11 (RM). While RM carefully trims DNA ends for repair, Lamassu chops up the host chromosome. Our study reveals how it is regulated to minimize damage, activating only during infection.
- Wow, a significant expansion of what we know about BREX. www.biorxiv.org/content/10.1...
- Reposted by artemisaevPhages evolve fast, or do they? In oysters, some stay identical for years. With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements. Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
- Reposted by artemisaevHow 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...
- Reposted by artemisaevDroplet-based Random Barcode Transposon-site Sequencing (Droplet RB-TnSeq) to characterize phage-host interactions biorxiv.org/content/10.1101/202…
- Reposted by artemisaevPrecisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise. Until now, using AccuSNV. Herui Liao trained an ML model based on our previous meticulously called SNVs. www.biorxiv.org/content/10.1...
- Reposted by artemisaevExcited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology. www.nature.com/articles/s41...
- Reposted by artemisaevYou like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range. @rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social www.nature.com/articles/s41...
- Reposted by artemisaevYprA family helicases provide the missing link between diverse prokaryotic immune systems biorxiv.org/content/10.1101/202…
- Reposted by artemisaevThe beautiful, ever-expanding universe of viral proteins targeting nucleotide immune signals! Paper by @reneechang.bsky.social in @cp-molcell.bsky.social on a nucleotide sponge www.cell.com/molecular-ce... and preprint by @doudna-lab.bsky.social on viral nucleases www.biorxiv.org/content/10.1...
- Reposted by artemisaevExcited to share our new preprint co-led by @jnoms.bsky.social! Here we reveal an exceptional diversity of viral 2H phosphodiesterases (PDEs) that enable immune evasion by selectively degrading oligonucleotide-based messengers. This 2H PDE fold has evolved striking substrate breath & specificity.
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- Reposted by artemisaevVery proud to have our lab’s first work published in @cp-cellhostmicrobe.bsky.social! In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes! Congrats to first author @luis840alberto.bsky.social ! www.cell.com/cell-host-mi... (1/3)
- My lab’s first preprint! We used functional metagenomics to identify phage defenses in human and soil microbiomes. We scaled these selections while maintaining accuracy, enabling us to examine 9 habitats for defense elements against 7 phages. www.biorxiv.org/content/10.1... 1/10
- Reposted by artemisaevRecurrent acquisition of nuclease-protease pairs in antiviral immunity biorxiv.org/content/10.1101/202…
- Reposted by artemisaevFirst preprint from the Nemudryi Lab! 🍾 In this work, we link antiviral immunity in bacteria and humans by showing that homologs of human Schlafen nucleases protect bacteria from phages. www.biorxiv.org/content/10.1...
- Reposted by artemisaev📢Preprint out! Excited to share my final work from the @soreklab.bsky.social! We mined phage dark matter using structural features shared by anti-defense proteins (viral tools that help phages bypass bacterial immunity) to guide discovery. Found 3 new families targeting immune signaling!
- Reposted by artemisaevNuclease-NTPase systems use shared molecular features to controlbacterial anti-phage defense biorxiv.org/content/10.1101/202…
- Reposted by artemisaevStructural insights into type I and type II Lamassu anti-phage systems biorxiv.org/content/10.1101/202…
- Reposted by artemisaevNew preprint: Modeling protein expression with explicit tRNA dynamics. We find that there's an optimum level of codon usage bias that maximizes expression. We also find charged rare tRNAs get fully depleted in late-stage bacteriophage T7 infection. www.biorxiv.org/content/10.1...
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- We performed a dedicated search of anti-CRISPR proteins targeting the model E. coli Type IE CRISPR-Cas system and revealed AcrIE9 as a potent inhibitor and the most widespread anti-CRISPR protein in enteric bacteria. www.biorxiv.org/content/10.1...
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