Jeremy Garb

Thanks for being part of it Melanie😊

Thank you Jens😊

Thanks François

I had so much fun making this project come to life!
Huge thanks to everyone who made it happen 💙 - especially my brilliant collaborators
David W. Adams, Eliane Hadas Yardeni, @mblokesch.bsky.social‬, and of course @soreklab.bsky.social‬

Our work shows that synthetic proteins can be designed to defeat bacterial immune systems.
This strategy could:
✅ Broaden the host range of therapeutic phages.
✅ Allow personalized phages for each patient’s infection.
✅ Unlock genetic engineering in “untouchable” bacteria for biotech + medicine.

It’s not just phages either.
We designed inhibitors for DdmDE, a system in Vibrio cholerae that usually clears plasmids from transformed cells.
Two of these binders conferred the plasmids with significant resistance against DdmDE-mediated plasmid clearance even in its native bacterial strain.

Now that we had binders against two defense systems, we engineered a single phage to carry two inhibitors.
➡️ This phage could overcome two defenses in the same bacterium.
This shows we can build “multi-resistant” phages for therapy.

We also built inhibitors against Avs1, a bacterial ancestor of human immune NLRs.
Synthetic binders blocked Avs1 activity—again, letting phages replicate in bacteria that co-express our binders with Avs1.

Using this workflow, we successfully identified multiple binders that inhibit Thoeris when co-expressed during infection ✅

To test candidate binders, and check if they successfully inhibit anti-phage defense systems, we built a 96-well transformation and phage-infection workflow (otherwise – far too many transformations!). This let us screen ~200 candidates at a time against a given system.

We started with the Thoeris system, where ThsB makes a signal (3′cADPR) that activates ThsA by binding its SLOG receptor domain.
We hypothesized that designing small proteins that bind the molecule-sensing site in the SLOG domain would disrupt its ability to perceive the signaling molecules.

What if we design proteins to disable these defenses?
Using AI-driven de novo protein design (RFdiffusion), we created small proteins (49–98 aa) that bind and block bacterial defense proteins 💻🤖🧬

Some background 📖
Bacteria are far from defenseless.
They carry dozens of anti-phage and anti-plasmid systems—CRISPR is just the tip of the iceberg.
➡️ This makes phage therapy often fail in patients.
➡️ It also makes many bacteria very hard to genetically engineer.

Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...

📢 New preprint alert!
We designed synthetic proteins that can block bacterial immune systems, allowing phages + plasmids to overcome natural defenses.
This could transform phage therapy + genetic engineering.
Here’s what we found 🧵
Preprint🔗: www.biorxiv.org/content/10.1...

@dinahoch.bsky.social dingazzz