Osterman Ilya

1/4 Bacterial immunity with “two-factor authentication”? Our new preprint by @monikajasnauskaite.bsky.social et al. reveals how DRT4 combines DNA synthesis with recognition of a phage protein to activate antiviral defense - a short thread below 🧵 BioRxiv: www.biorxiv.org/content/10.6...

Much of the functional biology encoded in genomes remains hidden in noncoding DNA. In a preprint out today, Patrick Hsu and team introduce COMPASS, a genomic language model-based approach to systematically map this underexplored sequence space.

A prophage-encoded anti-phage defence system that prevents DNA packaging by targeting the terminase complex | Nature Communications

Death and chemotaxis: Bacterial chemotaxis enables collective escape from phage predation Science Advances www.science.org/doi/10.1126/...

Viruses have parasites too. Our new preprint shows how phages use VIPR to silence parasitic satellites, and how the satellites fight back with its own decoy VIPR RNAs that redirect VIPR to DNA REP elements in the host genome!! www.biorxiv.org/content/10.6...

Very nice discovery from the Jackson, Bravo and Basel labs. Cleaved tRNA ends, loaded with an amino acid, activate a form of bacterial immunity

How does a single methyl group activate bacterial defence? Our new preprint, led by @pspatharas.bsky.social in collaboration with the group of @matthiaswilmanns.bsky.social, explains how a single DNA methylation event activates large retron assemblies. www.biorxiv.org/content/10.6...

1/1 How does a single methyl group activate bacterial defence? In my PhD work with @matthiaswilmanns.bsky.social and @typaslab.bsky.social, we reveal how this tiny DNA modification triggers retron disassembly and toxin activation. Now on bioRxiv: www.biorxiv.org/content/10.6...

LoL-align is out in @natmethods.nature.com! It aligns protein structures without superposition. More sensitive than TM-align and DALI, producing better alignments 5–20× faster. Now available in Foldseek! 📄 www.nature.com/articles/s41... 💾 github.com/steineggerlab/foldseek 🌐 search.foldseek.com

The legendary Symposium on the Immune System of Bacteria is coming to Cambridge, UK. Mark your calendars for 20-22 July 2027. Registration now open!

1/5 Telomerase has long been linked to chromosome maintenance in eukaryotes. Now, we show that telomerase-like activity is also present in bacteria, shedding new light on its ancient origins. Excited to share that our work on DRT10 is now out in @nature.com! www.nature.com/articles/s41...

Massive thanks to P. Yoon and, S. Lopez, @kshulgina.bsky.social, @clangeberg.bsky.social, @knottrna.bsky.social , @doudna-lab.bsky.social and to all our collaborators. Now on @biorxivpreprint.bsky.social www.biorxiv.org/content/10.6... 11/11

Heads-up! I’ll be starting my research group at MedUni Vienna in January 2027, with postdoc and PhD positions available soon. Looking for people interested in bacteria–phage interactions, bacterial defense systems, and phage anti-defense strategies. Please send your CV: anna.lopatina@univie.ac.at

Check out my preprint! We uncovered a neat story about the little understood story of hijacking transcription by phage D29! Super excited and grateful to work with everyone involved in this project.

Uncovering novel phage defense systems through genomic island analysis in Streptococcus thermophilus https://www.biorxiv.org/content/10.64898/2026.10.04.756616v1

New online! How bacterial immune systems sense phage infection

Our lab's first preprint! The antiphage protein Tiamat is an ATPase and DNase with homologs across the tree of life. What started as undergrad Shirley Yuan's summer project grew into a paper and a collaboration with @jpkbravo.bsky.social's group. Link: www.biorxiv.org/content/10.6...

Our story with @hobbslabutah.bsky.social discovering CBASS sensing of phage proteases out now in @science.org New data include CBASS recognition of diverse proteases beyond T4, and verifying CD-NTase activation loop cleavage as the trigger for defense in vivo www.science.org/doi/10.1126/...

Very excited to share the first preprint from my PhD with the community! This is also the first paper from the Plant Immunogenomics group with @galofir.bsky.social, so stay tuned for more! www.biorxiv.org/content/10.6... 1/n 🧵

Nicely executed study on phage anti-defence rdcu.be/M7mrq41uU7Ma

1/13 — New pre-print from the Sternberg Lab in collaboration with Leifu Chang's Lab! TnpB nucleases have repeatedly given rise to TldRs, nuclease-dead RNA-guided transcription factors. Here we define the biological role of one TldR clade in its native host. Story: www.biorxiv.org/content/10.6...

Super excited to share my postdoctoral work at @imbavienna.bsky.social @viennabiocenter.bsky.social - We discovered that some retrotransposons, or "jumping genes" 🧬, are able to spread from cell to cell via a new viral infectivity route. A short thread: 🧵👇 (1/7)

Better late than never. Congrats to former PhD trainee Shelby Andersen on the publication of RADS. RADS identifies antiphage defense systems connected to small serine recombinases. The question remains, why are defense systems often placed in this context? 🤔 journals.plos.org/plosbiology/...

A phage DUF669 protein mediates post-cleavage DNA repair against host CRISPR immunity | Nature Communications

New preprint from PhD student Yu Sun. TSR1 is a TIR effector specialised for CRISPR defence. It is an obligate dimer activated by cA3 and degrades its own activator using a ring nuclease domain. Perhaps the first confirmed dimeric TIR effector? www.biorxiv.org/content/10.6...

BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al. 📄 www.biorxiv.org/content/10.6... 🌐 bfvd.foldseek.com

Our paper on type II Panoptes is now published at PLOS Biology with new data on phage escapers - quite a step up in microbiology for our lab, led by Sabine Gruschow. Thanks to @erc.europa.eu for funding dx.plos.org/10.1371/jour...

Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/

Congratulations to @francoisrousset.bsky.social and colleagues, who discovered NIR—“NADase in bacterial immunity and vault ribonucleoproteins”—a new NAD⁺-depleting domain! NAD⁺ is involved in defense yet again, while its reconstitution by NARP1 was shown to help phages overcome this defense :)

Why did some #viruses evolve to be #giants while others did not? Our perspective piece on this topic with Eugene Koonin. www.pnas.org/doi/10.1073/...

It's finally published! What a journey @brownlab.bsky.social and I have been on with this one (ask me about it over a pint 🍻). Super excited to be able to say that it's finally out in Trends (author gift link to follow)! 🦠🧫 #phagesky

Chromatin structure controls defense island expression! Why do some systems defend on plasmids but fail natively? H-NS is key. Removing it boosts defense and overcomes anti-defense proteins but raises toxicity. Common lab strains still hide novel immunity modules! www.biorxiv.org/content/10.6...

UniProt is where most researchers start when they want to understand a protein. As of today, prokaryotic entries there will show something new: genomic context, powered by SeqHub, right in the Sequence section of the page.

Bacterial ribosomes can synthesize proteins encoded within their own RNA - WOW🔥 Very elegant and inspiring work from Shura Mankin's lab - Congratulations! www.nature.com/articles/s41...

Run AlphaFold2 locally in your browser via WebGPU, no installation needed, it's just a static webpage using your own GPU or CPU. Short proteins run in seconds. Larger ones are still slow: a 291-aa protein takes ~7 minutes on my M4 Pro. ❗It's just a PoC. 🌐 martin-steinegger.github.io/alphafold2-w...

🚨 ‼️ NEW PUBLICATION ‼️ While we start to know a lot about how bacterial genomes are organized in 3D, almost nothing is known about phage genome once it enters a bacterial cell. read the paper here: www.science.org/doi/10.1126/...

Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com

A phage communication peptide alters Bacillus subtilis colony development and promotes sporulation https://www.biorxiv.org/content/10.64898/2026.08.23.746533v1

@indrabekere.bsky.social probed a nucleotide library from bacterial & invertebrate signaling molecules in human cells, looking for new signaling. A great tool for mapping STING's preferences across cyclic nucleotides, incl. pyrimidine-purine hybrids.

Excited to share our paper with @savitski-lab.bsky.social, led by @tarabartolec.bsky.social, Karin Mitosch & Clément Potel, out now in @nature.com. We show that T7 phage broadly disables bacterial defenses using a unique ‘loose cannon’ protein kinase. www.nature.com/articles/s41...

1/5 How much phosphorylation can a single kinase deposit? In our new study with @typaslab.bsky.social out in @nature.com, phage T7's kinase (T7K) modifies almost all the E. coli proteome + more densely than all ~500 kinases do our own proteomes 🤯 www.nature.com/articles/s41...

pubmed.ncbi.nlm.nih.gov/42578370/

Today we are excited to introduce you to PanDA 🐼🐼🐼, a newly uncovered antiphage system!! Attendees at @SISB2026 would have heard a little about this from graduate student Ali Nabhani back in May, but we are now out here in preprint form and delighted to share more of the details. (Thread below)

Excited to share our story on diadenylate cyclases in bacterial immunity! Building on the discovery of Panoptes, we present Panoptoo: a DAC operon that uses cUA to guard against phage infection. Grateful to @daniellehaley.bsky.social and @kranzuschlab.bsky.social www.biorxiv.org/content/10.6...

The shared principles of human and bacterial antiviral immunity An honor to highlight remarkable discoveries from many labs over the past 12 years that unite previously disparate fields of how animal cells and prokaryotes defend against viruses. www.nature.com/articles/s41... rdcu.be/fzwyB

Do you need to analyze bacterial microscopy data and are looking for an all-in-one tool for Windows or macOS? Check out BactoMate by Lasse Hallenga and Philipp Popp! I'm happy that we were able to contribute to this great work. www.biorxiv.org/content/10.6...

DNA glycosylases are repair enzymes, essential to all cellular life. They find chemically damaged bases and remove them so DNA can be repaired. Today in Nature Microbiology, we show bacteria have repeatedly repurposed them into antiviral immune systems 🧵 www.nature.com/articles/s41...

If you are looking for web-based phage annotation, phage-annotation.org is live. Upload a genome to run Pharokka, Phold and Phynteny sequentially (see our recent protocols paper doi.org/10.1002/cpz1...). If you have feedback, please reach out Thanks to @ardc.edu.au for making this possible!

Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek