CSSB’s first flagship project “PLASMOFRACTION” has successfully deciphered membrane protein complexes in the malaria parasite Plasmodium falciparum.

Find out more: t1p.de/wthx2

@jankosinski.bsky.social, @embl.org, @uni-hamburg.de, @unituebingen.bsky.social, @fmp-berlin.de

Bacterial rRNAs are highly modified, but their functions are often mysterious. Zac Park says that methylation of 16S rRNA by MraW(RsmH) enhances translation of structured mRNAs. Thus, mRNA structure and rRNA modifications likely co-evolved to fine-tune protein dosage.
www.biorxiv.org/content/10.6...

Structures of the QatBC complex from Angela Gao and Doug Wassarman in our group reveal an evolutionary link between QatABCD and Type IV CBASS and a role for protein deazguanylation in diverse anti-phage defense systems

www.nature.com/articles/s41...

www.science.org/doi/10.1126/...

Bacteriophages are in a constant arms race with bacteria 🦠 The Phage ORFeome pooled library from the Aaron Whiteley lab contains phage proteins that activate antiphage defense systems — a tool to dissect the mechanisms of bacterial immunity. Aaron Whiteley

Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity - Nature Communications Phages employ diverse counter-defense strategies to overcome bacterial immune systems. Here, the authors reveal that the phage homing nuclease SegB facilitates immune evasion by promoting the segmenta...

Happy to share our new work on how phages escape bacterial immunity.

We show that a phage homing endonuclease drives segmental amplification of anti-defense genes, pointing to a versatile and rapid mode of adaptation.

www.nature.com/articles/s41...

#PhageSky #MicroSky

Those amazing #phages 🦠 figured out 5mC chemistry before we did:
📄 Out today in @MolecularCell we describe a 5mC-selective #deaminase family in environmental phage genomes with broad applications for #5base #sequencing
#epigenetics #DNAmethylation #genomics #NGS 🧬🧪
www.cell.com/molecular-ce...

Very proud of this work and all the efforts from my team and collaborators on this! You can now use DGRs for in vivo targeted hypermutagenesis in E. coli. We also included some early proof of concept in Yeast thanks to @seth-shipman.bsky.social !

Excited to share our new findings in @science.org on how the DRT3 bacterial defense system uses a reverse transcriptase that builds DNA repeats without a nucleic acid template. Microbes never cease to amaze!

www.science.org/doi/10.1126/...

Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology Diversity-generating retroelements are engineered for directed evolution in E.coli.

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

Thank you Quanta Magazine for highlighting our studies on the bacterial immune system!

How artificial intelligence is reengineering protein engineering | Science www.science.org/eprint/666XR...

Dual cytosine modification through hydroxylation and arabinofuranosylation in phages - Nature Chemical Biology He et al. identified a cytosine hypermodification pathway in phage HY126. This pathway involves prereplicative deoxycytidine monophosphate hydroxylation and arabinofuranosylation, followed by postrepl...

A new paper reports a cytosine hypermodification pathway in phage HY126 that confers nuclease resistance

www.nature.com/articles/s41...

What if AI could invent enzymes that nature hasn’t seen? 👩‍🔬🧑‍🔬

Introducing 🪩 DISCO: Diffusion for Sequence-structure CO-design

📝 Blog: disco-design.github.io
📄 Paper: arxiv.org/abs/2604.05181
💻 Code: github.com/DISCO-design...

Nucleoid-associated proteins sense phage-induced genome damage to elicit abortive infection www.biorxiv.org/content/10.64898/2026.04...

Would carving of the mechanism of Metis antiphage defense

Our current understanding of the Metis defense system - carved in wood

By @naamalila.bsky.social

www.biorxiv.org/content/10.1...

A big advance in the field of bacterial immunity, from the Bernheim and Laub labs

Fantastic results and fantastic tool - Congratulations and Thank you👏👏👏

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_...

The PhageExpressionAtlas just made it to bioRxiv. Visually explore the transcriptomes of phage-host interactions or harness the database for analysis across infections! Please leave feedback, which functionalities/data you find missing.
Preprint:
www.biorxiv.org/content/10.6...

#phagesky #microsky

AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network Nature Methods - ROCKET improves experimental structure elucidation by integrating implicit structural knowledge from OpenFold, a trainable reimplementation of AlphaFold2, with X-ray...

ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH
Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15

Bacterial 2′,3′-cGAMP activates a SAVED effector to form membrane-disrupting filaments and restrict phage replication Tak et al. discover that bacteria use 2′,3′-cGAMP, the same signaling molecule employed by mammalian cGAS-STING, for phage defense. In response to phage, 2′,3′-cGAMP activates filament formation of Ca...

Happy to share the final version of my postdoc work on bacterial CBASS immunity with @aaronwhiteley.bsky.social published in @cp-cellhostmicrobe.bsky.social

www.cell.com/cell-host-mi...

How do you kill a MRSA superbug armed with 15 different anti-phage defense systems? You make a smarter phage. Check out our latest preprint on overcoming bacterial immunity using defense-guided engineering to build durable therapeutic phage cocktails! Led by Sarah Voss. doi.org/10.64898/202...

RNAse protects from RNA-phage - smart strategy:) Congratulations Arina and Jens!

Generalist biological artificial intelligence in modeling the language of life - Nature Biotechnology This Review discusses the promises and pitfalls of biological AI algorithms and presents a vision for generalist biological artificial intelligence, in which models can perform diverse tasks across bi...

Generalist biological artificial intelligence in modeling the language of life - @rajpurkar.bsky.social @erictopol.bsky.social go.nature.com/3NdkqaE

FEBS Press The bacterial dynamin-like protein DynA from Bacillus subtilis plays a key role in phage defense. It binds the plasma membrane through a unique paddle domain in its D1 subunit. This membrane associat...

Binding of Bacillus subtilis dynamin‐like protein DynA to the bacterial membrane is essential for effective phage defense - Shafqat - 2026 - The FEBS Journal - Wiley Online Library febs.onlinelibrary.wiley.com/doi/full/10....

Simultaneous inhibition of bacterial virulence and anti-phage defense systems by synergistic bacteriophage counter-defense proteins - The EMBO Journal Bacteriophages have evolved diverse inhibitors targeting key bacterial processes, including virulence and anti-phage defense systems, which could inspire novel antimicrobial strategies and enhance pha...

Simultaneous inhibition of bacterial virulence & anti-phage defense by synergistic bacteriophage counter-defense proteins:
Shuai Le, Haihua Liang et al show how Dap2 sequesters T3SS activators & prevents Pseudomonas host from inactivating a key phage endonuclease
link.springer.com/article/10.1...

QR code to access 'Structural diversification of phage tail fibres enables recognition of diverse type IV pili'

New paper showing how tailed #phages recognize diverse #Pseudomonas #T4P! Outstanding work by PhD candidate Ikram Qaderi, building on work started a decade ago during my sabbatical in the McArthur lab and in collaboration with the Guarné lab, now at #McGill. @mcmasteriidr.bsky.social

Figure 1

Re-evaluating the role of hok/Sok in T4 phage defense #micropublication #biology #data #caltechlibrary #Escherichiacoli #PhenotypeData #ReplicationUnsuccessful micropublication.org/journals/biology/micropu...

New preprint: Cyclic tri-adenylate signalling by a Panoptes anti-phage guard system with a CARF-TM effector. Great work led by Sabine Grüschow
www.biorxiv.org/content/10.6...

Bacteriophage data on capsular Klebsiella bacteria barcoded library

New paper 🔔

Collaboration
@sullivan-lab.bsky.social
Marissa Gittrich led the work

Klebsiella phage biology has focused almost entirely on capsulated strains, but capsule loss is the #1 resistance mechanism under phage predation. We used a naturally acapsular host to reveal the receptor landscape