Osterman Ilya
@ostermanilya.bsky.social
📤 401
📥 340
📝 101
Senior Research Associate, microbiologist, biochemist, The Sorek lab, Weizmann Institute of Science
pinned post!
🚨After 4 fantastic years in the Sorek lab
@soreklab.bsky.social
, I’ll be starting my own group at EMBL
@embl.org
bl.org
Hamburg.
www.embl.org/groups/oster...
Metabolism-driven immunity: phages, metabolites, and discovery of new enzymes, molecules, and pathways 🦠🧬
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Osterman Group – Metabolism-driven immunity
https://www.embl.org/groups/osterman/
26 days ago
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Osterman Ilya
Shicheng Guo
1 day ago
Discover Hna, a key anti-phage defense in prokaryotes. Forms auto-inhibited complex, then activated by phage factor for DNA degradation, foiling phage attacks! PMID:42151145, Nat Commun 2026, @NatureComms
https://doi.org/10.1038/s41467-026-73157-2
#Medsky
#Pharmsky
#RNA
#ASHG
#ESHG
🧪
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Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system | Nature Communications
Prokaryotic organisms have evolved unique strategies to acquire immunity against the constant threat of bacteriophage (phage) and mobile genetic elements. Hna is a broadly distributed anti-phage immune system that confers resistance against diverse phage by eliciting an abortive infection response. Using a combination of biochemistry, cryo-electron microscopy, and single-molecule fluorescence imaging, we reveal that Hna functions as a 3’—5’ single-stranded DNA exonuclease that forms an auto-inhibited dimer under physiological ATP concentrations. Biochemical and mutational analyses demonstrate that Hna catalytic outputs are governed by kinetic partitioning between ATPase and nuclease active sites. Disruption of this balance enhances DNA cleavage and causes cellular toxicity. Furthermore, we show that a phage-encoded single-stranded DNA-binding protein (5 A SSB) destabilizes the autoinhibited Hna dimer and shifts catalytic partitioning toward dysregulated nuclease activation. Conversely,
https://doi.org/10.1038/s41467-026-73157-2
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Osterman Ilya
Shicheng Guo
2 days ago
Replaced yeast telomeres with Escherichia phage N15's prokaryotic TelN/tos system in Saccharomyces cerevisiae. Over 1 billion years of evolution challenged! PMID:42151157, Nat Commun 2026, @NatureComms
https://doi.org/10.1038/s41467-026-73335-2
#Medsky
#Pharmsky
#RNA
#ASHG
#ESHG
🧪
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Engineering yeast chromosomal telomeres with a bacteriophage system | Nature Communications
All eukaryotes, including yeast, plants, animals and humans, possess linear chromosomes. The conserved eukaryotic telomere-telomerase systems, originated and evolved over 1 billion years, protect the chromosomal ends and regulate critical physiological functions through complex networks. In this study, we replace the endogenous eukaryotic telomeres in the single-chromosome yeast Saccharomyces cerevisiae with the prokaryotic telomere system TelN/tos from the Escherichia phage N15, which forms a closed hairpin structure, by interrupting the MRX/Sae2 pathway. The prokaryotic telomeres effectively protect linear chromosomal ends and prevent genetic instability. Through adaptive evolution, we identify yeast strains harboring additional mutations (TEL1 and CYR1) that restore functional MRX/Sae2 activity, thereby improving host fitness and meiotic capacity. Interestingly, the two-associated TelN/tos telomeres position deeper into chromosomes and exhibit increased interactions with their adjac
https://doi.org/10.1038/s41467-026-73335-2
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Osterman Ilya
Nature Microbiology
4 days ago
#NatMicroPicks
Phage-to-phage dialogue! 🗨️💬 Arbitrium peptide signaling systems in bacteriophages exhibit cross-communication where peptides can influence non-cognate receptors to promote lysogeny
#MicroSky
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
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Arbitrium phages can manipulate each other’s lysis/lysogeny decisions
Arbitrium phages belonging to different species and genera can influence each other’s infection dynamics by secreting chemically similar, non-cognate signal peptides. These findings indicate that arbi...
https://www.cell.com/cell/fulltext/S0092-8674(26)00227-8
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Osterman Ilya
Tominaga K. (tomiken)
3 days ago
Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase | Science
https://www.science.org/doi/abs/10.1126/science.aed1656?af=R
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Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase
Defense-associated reverse transcriptases (DRTs) are widespread bacterial antiphage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), ...
https://www.science.org/doi/10.1126/science.aed1656
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Osterman Ilya
Molecular Cell
3 days ago
The DdmDE defense system eradicates plasmids by target-centered bidirectional ssDNA loop extrusion and site-specific cleavage
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The DdmDE defense system eradicates plasmids by target-centered bidirectional ssDNA loop extrusion and site-specific cleavage
Yang et al. reveal a dynamic DdmDE-mediated plasmid clearance pathway. Transient DNA bubbles permit promiscuous DdmE binding, while target specificity arises from slower dissociation at matched sites. DdmE then recruits a DdmD dimer to drive target-centered, bidirectional dsDNA unwinding. Free DdmD subsequently coats extruded ssDNA to enable site-specific endonucleolytic cleavage.
http://dlvr.it/TT6wh6
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Osterman Ilya
Kranzusch Lab
6 days ago
@ohadroth.bsky.social
and
@soreklab.bsky.social
discover bacterial enzymes that cleave the immune signal 2'cADPR explaining the mystery of XopQ virulence proteins in plant pathogens. Beautiful results mirroring phage inhibition of 2'- and 3'cADPR in bacteria! 🌱✂️
www.biorxiv.org/content/10.6...
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More discoveries from the NAD world: plant pathogens cleave 2′cADPR to suppress the immune response! Congratulations to
@ohadroth.bsky.social
and colleagues 👏
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6 days ago
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Osterman Ilya
phy_papers
16 days ago
Raw defines a TIR-fold cADPR hydrolase cooperating with dSarm in development and axon degeneration
https://pubmed.ncbi.nlm.nih.gov/42243876/
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Osterman Ilya
Tominaga K. (tomiken)
9 days ago
Bacteriophages hijack 2′,3′-cNMPs to enhance transposase-mediated phage DNA integration in Acinetobacter baumannii | Science Advances
https://www.science.org/doi/full/10.1126/sciadv.aec7770?af=R
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Bacteriophages hijack 2′,3′-cNMPs to enhance transposase-mediated phage DNA integration in Acinetobacter baumannii
Bacteriophages hijack 2′,3′-cNMPs in bacteria to enhance infections.
https://www.science.org/doi/10.1126/sciadv.aec7770
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Osterman Ilya
Jack Bravo
9 days ago
Very happy to share this preview article written by my postdoc Danny on exciting recent work from
@ostermanilya.bsky.social
and
@soreklab.bsky.social
. New bacterial immunity, phage countermeasures, and a double pun combo in the title.
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Osterman Ilya
Cell Host & Microbe
10 days ago
NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back Preview of work IDing aRES, bacterial proteins that deplete cellular NAD+, generating products that cannot be utilized by phage NAD+ regeneration pathways
www.cell.com/cell-host-mi...
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NAD to the bone: How bacteria put phages under aRES-t … and how phages fight back
In this issue of Cell Host & Microbe, Osterman et al. discover aRES, a new family of bacterial immune proteins that deplete cellular NAD+, generating cleavage products that cannot be utilized by canon...
https://www.cell.com/cell-host-microbe/abstract/S1931-3128(26)00206-4
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Osterman Ilya
Sofya Garushyants
10 days ago
Our paper on the YprA family of helicases and their roles in bacterial defence is now out! We describe ARMADA, a defence system synergise with Druantia and show that both systems spread horizontally on a novel type of mobile genetic element that we call SPIDERs
www.sciencedirect.com/science/arti...
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YprA-family helicases provide the missing link between diverse prokaryotic immune systems
Bacteria and archaea possess an enormous variety of antiviral immune systems that often share homologous proteins and domains. YprA-family helicases a…
https://www.sciencedirect.com/science/article/pii/S1931312826002088
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Osterman Ilya
Paul Rainey
10 days ago
Koonin & team dive deep into YprA-family defence systems that define “SPIDER” elements: satellite phage-like defence islands that overlap with the GIs we showed are transferred by jumbo phages. They're packed with ecologically relevant genes. The stuff that moves matters!
doi.org/10.1016/j.ch...
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Redirecting
https://doi.org/10.1016/j.chom.2026.05.015
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Osterman Ilya
Ákos T Kovács
11 days ago
Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity
@natmicrobiol.nature.com
from Michael Laub & Abel Garcia-Pino
www.nature.com/articles/s41...
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Bacterial cell division protein FtsZ complexes with a phage protein to activate bacterial immunity - Nature Microbiology
The activation of an antiphage defence system relies on host factors targeted by phages, a mechanism analogous to the way that eukaryotic innate immune systems detect pathogen-induced perturbations of...
https://www.nature.com/articles/s41564-026-02384-6
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Human immune proteins protect against phage infection - fantastic hypothesis and fantastic discovery!
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10 days ago
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Osterman Ilya
The EMBO Journal
13 days ago
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...
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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 ...
https://link.springer.com/article/10.1038/s44318-026-00831-y
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Osterman Ilya
Rafal Mostowy
13 days ago
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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Osterman Ilya
Wilson Lab
19 days ago
www.nature.com/articles/s41...
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A natural depsipeptide antibiotic binds the E-site of the bacterial ribosome - Nature
Improved fractionation strategies can identify antibiotics with previously unseen scaffolds and mechanisms, exemplified by manikomycin from Streptomyces rimosus, which acts by targeting the E-site of ...
https://www.nature.com/articles/s41586-026-10589-2
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Osterman Ilya
Cell Host & Microbe
20 days ago
Bacteria vs phage: new layers in NAD+ centric arms race aRES is bacterial protein that blocks phage infection by cleaving NAD+ into ADPR-1P & nicotinamide. Phages counter using NAD+ reconstitution pathway w/ADPR-1P & nicotinamide as substrates
www.cell.com/cell-host-mi...
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Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases
Osterman et al. describe a bacterial defense protein that, once triggered by the phage DNA polymerase, blocks infection by cleaving NAD+ into ADPR-1P and nicotinamide. They show how phages counter thi...
https://www.cell.com/cell-host-microbe/abstract/S1931-3128(26)00180-0
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Osterman Ilya
Sorek Lab
20 days ago
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...
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Osterman Ilya
Romi Hadary
20 days ago
Excited to see our work out in
@natmicrobiol.nature.com
! We uncovered broad functional diversity within phage sponge families🧽. Huge thanks to all coauthors and brilliant collaborators
@kranzuschlab.bsky.social
@reneechang.bsky.social
!
www.nature.com/articles/s41...
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Osterman Ilya
Shicheng Guo
23 days ago
Phage T4 boosts defense with 2 glucosyltransferases adding glucose to 5-hmC on DNA to ev… PMID:42206360, Nucleic Acids Res 2026, @NAR_Open @OTSociety @NAR_Open
https://doi.org/10.1093/nar/gkag531
#Medsky
#Pharmsky
#RNA
#ASHG
#ESHG
🧪
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https://doi.org/10.1093/nar/gkag531
No description available
https://doi.org/10.1093/nar/gkag531
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Osterman Ilya
Sorek Lab
24 days ago
Happy to see the paper out in Cell Host & Microbe. congratulations Ilya!
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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...
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24 days ago
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Another cool phage enzyme discovery! It degrades Thoeris signaling molecules into ADPR. Congrats to Miguel and all involved 🧬
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25 days ago
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🚨After 4 fantastic years in the Sorek lab
@soreklab.bsky.social
, I’ll be starting my own group at EMBL
@embl.org
bl.org
Hamburg.
www.embl.org/groups/oster...
Metabolism-driven immunity: phages, metabolites, and discovery of new enzymes, molecules, and pathways 🦠🧬
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Osterman Group – Metabolism-driven immunity
https://www.embl.org/groups/osterman/
26 days ago
10
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reposted by
Osterman Ilya
Shicheng Guo
30 days ago
PhaBOX2 revolutionizes metagenomic analysis with unified tools for viral discovery & classification, expanding beyond phage detection! PMID:42023515, Nucleic Acids Res 2026, @NAR_Open
https://doi.org/10.1093/nar/gkag382
#Medsky
#Pharmsky
#RNA
#ASHG
#ESHG
🧪
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https://doi.org/10.1093/nar/gkag382
No description available
https://doi.org/10.1093/nar/gkag382
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Osterman Ilya
bioRxiv Microbiology
28 days ago
Computational prediction resolves thousands of homooligomeric phage protein structures
https://www.biorxiv.org/content/10.64898/2026.05.24.727406v1
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Osterman Ilya
KhongSam Chia
about 1 month ago
Preprint Alert 🚨
@philcarella.bsky.social
lab stepping into TIR-ritory!! Project started by me but finished by talented PhD student
@ebkennedy.bsky.social
(Please follow her), with contribution from Zhao He and
@jonathandgjones.bsky.social
We investigated EDS1-dependency of TIR domain. See thread👇
add a skeleton here at some point
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Osterman Ilya
Sternberg Lab
about 1 month ago
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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Osterman Ilya
Sorek Lab
about 1 month ago
A nice piece at
@science.org
covers the exploding field of bacterial immunity, and how it led to the understanding that components of the human immune system evolved from bacterial defenses against phage
www.science.org/content/arti...
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Ancient wars between microbes gave us key immune defenses
A better understanding of battles between bacteria and viruses could inspire new medicines
https://www.science.org/content/article/ancient-wars-between-microbes-gave-us-key-immune-defenses
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Osterman Ilya
Cell Host & Microbe
about 1 month ago
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...
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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 ...
https://www.cell.com/cell-host-microbe/abstract/S1931-3128(26)00170-8
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Osterman Ilya
STCmicrobeblog
about 1 month ago
#RNASky
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New tool decodes the structures and motifs of RNA
https://nachrichten.idw-online.de/2026/05/20/new-tool-decodes-the-structures-and-motifs-of-rna
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Osterman Ilya
Shicheng Guo
about 1 month ago
Phage encodes a sponge protein blocking bacterial TIR-Caspase immune signaling, inhibiting type IV Thoeris. Discovered through phage mating assays. PMID:41968157, Nat Commun 2026, @NatureComms
https://doi.org/10.1038/s41467-026-71527-4
#Medsky
#Pharmsky
#RNA
#ASHG
#ESHG
🧪
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A phage-encoded sponge protein suppresses bacterial TIR-Caspase immune signaling | Nature Communications
Triggering immune response through generation of signal molecules is a common immune strategy across all domains of life. In the bacterial type IV Thoeris anti-phage system, a Toll/interleukin-1 receptor (TIR)-domain protein produces adenosine 5’-diphosphate-cyclo[N7:1”]-ribose (N7-cADPR) as the immune signal to activate a Caspase-like effector. Here, we identified an inhibitor of type IV Thoeris through a phage mating assay that allows a sensitive phage to acquire anti-defense genes from related resistant phages. The inhibitor (hereafter TadIV-1) functions as a sponge that sequesters the N7-cADPR signal to inhibit Caspase activation. Structural analyses of TadIV-1 indicate a distinctive signal binding mechanism, wherein the binding pocket comprises its N-terminal flexible loop. In addition, phages lacking TadIV-1 can escape type IV Thoeris sensing through mutation in the capsid vertex protein. Collectively, this work expands the phage anti-defense arsenal with a unique immune signal s
https://doi.org/10.1038/s41467-026-71527-4
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Osterman Ilya
Julia Frunzke
about 1 month ago
Registration opened for our International Symposium of SPP 2330! This is going to be phage-tastic meeting in Berlin! Highlight of the second funding period!
@spp2330.bsky.social
,
@dfg.de
add a skeleton here at some point
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Osterman Ilya
Luuk Loeff
about 1 month ago
Happy to share our latest pre-print on the Druantia defense system. We find that Type III Druantia uses a cooperative helicase-nuclease mechanism to sense and degrade replication-associated forked DNA structures.
www.biorxiv.org/content/10.6...
A🧵
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https://www.biorxiv.org/content/10.64898/2026.05.13.724313v1
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Osterman Ilya
Sternberg Lab
about 1 month ago
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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Osterman Ilya
Mart Krupovic
about 1 month ago
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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Osterman Ilya
Ryan Cook
about 2 months ago
During my PhD,
@milja001.bsky.social
and I started counting phage genomes, and tried to make them available in useful formats with useful metadata. We also described the extent of sequenced phage genomes at the time. Five years on, we've had a look at what's changed
www.biorxiv.org/content/10.6...
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https://www.biorxiv.org/content/10.64898/2026.05.06.722914v1
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Osterman Ilya
Rob Edwards
about 2 months ago
Want to find
#prophage
in your
#bacteria
genomes? We built PhiSpy a long time ago, and now we've created a new web page for it:
linsalrob.github.io/PhiSpyWeb/
Best of all, the data never leaves your computer!
#phage
#phagesky
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PhiSpyWeb – Browser-based Prophage Prediction
Browser-based prophage prediction using PhiSpy, Pyodide, and WebAssembly
https://linsalrob.github.io/PhiSpyWeb/
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Osterman Ilya
Julia Frunzke
about 2 months ago
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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Osterman Ilya
bioRxiv Biochemistry
about 2 months ago
TIR-like NADases act in bacterial immunity and the RNA vault
https://www.biorxiv.org/content/10.64898/2026.05.01.722283v1
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Osterman Ilya
laurelrobbins.bsky.social
about 2 months ago
I’m thrilled to share an update to our work on bacterial NACHT domain containing proteins! In our last preprint, we reported that bNACHT11 is activated by multiple phage proteins. We’ve now expanded this work with structural insight and investigation of programmed cell death following activation.
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https://www.biorxiv.org/content/10.1101/2024.12.17.629029v2
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Osterman Ilya
Tera Levin
about 2 months ago
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/
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Osterman Ilya
Kenneth Loi
about 2 months ago
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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Osterman Ilya
Nature Microbiology
about 2 months ago
Out Now! Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity
#MicroSky
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Nuclease–NTPase antiphage defence systems use conserved molecular features to control bacterial immunity
Nature Microbiology, Published online: 27 April 2026; doi:10.1038/s41564-026-02312-8A large-scale, comparative cell biology and biochemical screen defines the molecular features controlling antiphage defence systems that encode nuclease effectors and accessory NTPase proteins.
https://go.nature.com/4tD1DW4
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reposted by
Osterman Ilya
Wilson Lab
about 2 months ago
www.nature.com/articles/s41...
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The regulation, function and disease relevance of cytoplasmic tRNAs - Nature Reviews Molecular Cell Biology
This Review discusses the expression and maturation of human cytoplasmic tRNAs and recent insights into their regulation of translation. The authors also explore emerging roles of tRNAs in ribosome-as...
https://www.nature.com/articles/s41580-026-00963-3
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Osterman Ilya
Joe Bondy-Denomy
about 2 months ago
Phage community: our plasmids for executing phage transposon mutagenesis are now on AddGene and I would love for you to try it out! It is powerful for ID'ing all essential genes and knocking out all non-essentials in a single experiment :) New exp here:
www.addgene.org/browse/artic...
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Osterman Ilya
Michal Kolář
2 months ago
Our latest contribution is out! In this highly collaborative paper, we show that tRNAs with a 4-base-pair anticodon stem are surprisingly frequent across organisms. Our atomistic MD simulations reveal the role of the 5th base pair.
academic.oup.com/nar/article/...
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Frequent occurrence and predicted functions of tRNAs with 4-base-pair anticodon stems in bacteria: extended superwobble hypothesis
Abstract. Recently, a tRNATrpCCA with a 4-base-pair (bp) anticodon stem (AS) was shown to efficiently recognize a near-cognate UGA codon in unicellular euk
https://academic.oup.com/nar/article/54/7/gkag327/8659125?login=false
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Osterman Ilya
Shicheng Guo
2 months ago
Mycobacterial NHEJ crucial for phage defense. Linking DNA repair to viral resistance, study highlights NHEJ's vital role. PMID:41603729, Nucleic Acids Res 2026, @NAR_Open @OTSociety @NAR_Open
https://doi.org/10.1093/nar/gkag066
#Medsky
#Pharmsky
#RNA
#ASHG
#ESHG
🧪
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https://doi.org/10.1093/nar/gkag066
No description available
https://doi.org/10.1093/nar/gkag066
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