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Sorek Lab @soreklab.bsky.social · 17/06/2026

Back to bacterial immunity: We recently discovered a Thoeris system that relies of 2’cADPR signaling to protect against phages (see previous thread). We never find XopQ co-occurring with this bacterial defense system – because XopQ cleaves 2’cADPR and inhibits immunity bsky.app/profile/erez...

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Sorek Lab @soreklab.bsky.social · 17/06/2026

Together with our collaborators at the Max Planck Institute for Plant Breeding Research (thank you Paul Schulze-Lefert and Jane Parker!) we showed that XopQ prevents accumulation of 2’cADPR in plant cells, and allows plant pathogens to overcome TIR immunity during infection

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Sorek Lab @soreklab.bsky.social · 17/06/2026

XopQ belongs to a family of nucleoside hydrolase enzymes. Ohad measured the Michaelis-Mentin constants for XopQ and found it to be the most efficient enzyme of this family, working in a near diffusion limited rate. It is very specific to 2’cADPR – doesn’t cleave related molecules such as 3’cADPR

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Sorek Lab @soreklab.bsky.social · 17/06/2026

The answer is yes. Dr Ohad Roth in the lab discovered that XopQ, a protein secreted into plant cells by many plant pathogens, is an enzyme that cleaves the TIR-produced signaling molecule 2’cADPR. XopQ was discovered 22 years ago, but until now its function was obscure

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Sorek Lab @soreklab.bsky.social · 17/06/2026

In the plant immune system, TIR-domain proteins work similarly: they recognize infection, then produce signaling molecules, which activate a downstream immune complex that contains the protein EDS1

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Sorek Lab @soreklab.bsky.social · 17/06/2026

For several years now we study the Thoeris bacterial defense system, which employs TIR domains. We showed that Thoeris TIR proteins respond to phage infection by producing signaling molecules. These molecules activate a second protein in the Thoeris system, which acts to prevent phage replication

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Sorek Lab @soreklab.bsky.social · 07/04/2026

Our current understanding of the Metis defense system - carved in wood By @naamalila.bsky.social www.biorxiv.org/content/10.1...

Would carving of the mechanism of Metis antiphage defense

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Sorek Lab @soreklab.bsky.social · 29/01/2026

Using an Alphafold co-folding screen, we found that some phages also encode small proteins that directly bind the defensive RES domain and inhibit aRES ability to cleave NAD

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Sorek Lab @soreklab.bsky.social · 29/01/2026

Then, we found that some phages evolved an extended NARP1 pathway, which includes a phosphatase. This phosphatase removes the additional phosphate from ADPR, and now NARP1 can work again

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Sorek Lab @soreklab.bsky.social · 29/01/2026

Now, we found defense genes that rely on RES domains, which also cleave NAD+ but leave a phosphate group on ADPR This mode of NAD+ cleavage renders phage NARP1 inactive, because the pathway cannot use ADPR-1P as a substrate So this system, named aRES, defends from phages even if they encode NARP1

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Sorek Lab @soreklab.bsky.social · 29/01/2026

Two years ago we discovered that many phages encode a pathway that can rebuild NAD directly from ADPR and Nam, the debris left after NAD was broken by bacterial defenses. We called this pathway NAD reconstitution pathway 1 - NARP1 (Osterman, Nature 2024)

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Sorek Lab @soreklab.bsky.social · 29/01/2026

Many bacteria degrade their entire NAD+ pool when they sense phage infection. NAD depletion deprives the phage of this essential molecule and prevents it from replicating The bacterial defense systems typically break NAD into two molecules: ADPR and Nam

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Sorek Lab @soreklab.bsky.social · 04/12/2025

Preprint: Systematic discovery of TIR-based immune signaling systems in bacteria Conservation of TIR-derived signals accross the tree of life! We found bacterial TIR immune systems that signal via canonical cADPR (like in humans) and 2'cADPR (a plant immune signal). Documented 11 Thoeris types

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Sorek Lab @soreklab.bsky.social · 14/11/2025

Congratulations to Sorek lab alumnus Nitzan Tal, who won the prestigious 2025 Science & SciLifeLab prize for the best PhD thesis in Systems Biology! 💫 Read her Prize Assay, published in the journal Science today www.science.org/doi/10.1126/... @nitzantal.bsky.social

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Sorek Lab @soreklab.bsky.social · 06/11/2025

Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides tinyurl.com/ch3damp We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity Revealed by the amazing Ilya Osterman. See his thread below👇

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Sorek Lab @soreklab.bsky.social · 02/09/2025

Together with Melanie Blockesch and David Adams from EPFL, we show that plasmids expressing synthetic anti-defense proteins successfully transform and become retained in V. cholerae, enabling stable plasmid maintenance 7/n

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Sorek Lab @soreklab.bsky.social · 02/09/2025

Engineering phages to express multiple anti-defense peptides in a row enabled them to infect bacteria with multiple defense systems. We believe this approach will allow using phages as therapy against bacteria that encode many defense systems 5/n

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Sorek Lab @soreklab.bsky.social · 02/09/2025

We developed a high-throughput screening approach to assess the new designs. The technique rapidly detects peptides that efficiently inhibit bacterial defenses in vivo. We showed in vitro that the peptides tightly bind the defense proteins in nanomolar range affinity, and inhibit their activity 4/n

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Sorek Lab @soreklab.bsky.social · 02/09/2025

New AI tools now allow the design of peptides that bind protein targets. We used RFdiffusion to design peptides that bind active sites of defense system proteins. These peptides do not exist in nature – they are completely “made up”! 3/n

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Sorek Lab @soreklab.bsky.social · 25/08/2025

Preprint: We discovered phage proteins that sequester diverse immune signaling molecules, including cUMP, cCMP, and N7-cADPR The first viral sponges to inhibit Pycsar and type IV Thoeris Congrats to talented leading author Romi Hadary! Read her thread to learn more about our findings

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Sorek Lab @soreklab.bsky.social · 30/07/2025

Some immune proteins produce altered nucleotides that poison viral replication. Viperin proteins, conserved from bacteria to humans, modify nucleotides to remove their 3’ OH moiety. The modified nucleotide is incorporated into the replicating viral RNA, and terminates viral replication 14/16

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Sorek Lab @soreklab.bsky.social · 30/07/2025

As one could expect, viruses developed a huge variety of molecular techniques to evade or suppress host nucleotide signaling. We tried to summarize these in one (rather complex) figure 13/16

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Sorek Lab @soreklab.bsky.social · 30/07/2025

Bacteria, masters of innovation and diversity, employ other immune pathways that use the nucleotide pool for substrates. Type III CRISPR systems build large “rings” of adenosines, while the Pycsar system produces cyclic CMP and cyclic UMP as immune signaling molecules 12/16

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Sorek Lab @soreklab.bsky.social · 30/07/2025

Bacterial and plant immune TIRs produce “exotic” immune signaling molecules. In some cases, these are versions of cyclic ADPR (cADPR). In other cases the signaling molecules comprise ADPR conjugated to histidine (His-ADPR) or ADPR conjugated to ATP 11/16

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Sorek Lab @soreklab.bsky.social · 30/07/2025

Bacteria and plants share immune pathways that rely on ADP-ribose (ADPR) derivatives as immune signaling molecules. These molecules are produced by TIR proteins, which are enzymes that process NAD to generate signaling molecules 10/16

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Sorek Lab @soreklab.bsky.social · 30/07/2025

The cGAS-STING pathway evolved from a large family of bacterial defense systems called CBASS (cyclic oligonucleotide based antiphage signaling systems). These systems produce a variety of cyclic di-nucleotides and tri-nucleotides as signaling molecules. About 15% of all bacteria encode CBASS 9/16

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Sorek Lab @soreklab.bsky.social · 30/07/2025

The human cGAS-STING pathway uses the nucleotides GMP and AMP as building blocks to generate the immune signaling molecule cyclic GMP-AMP (cGAMP). In other animals, cGAS-like proteins (cGLRs) produce alternative molecules, for example cyclic UMP-AMP 8/16

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Sorek Lab @soreklab.bsky.social · 30/07/2025

In bacteria, some defense systems convert ATP and deoxy-ATP to their inosine derivatives – ITP and dITP. This halts phage replication in a way that is not yet completely understood 5/

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Sorek Lab @soreklab.bsky.social · 30/07/2025

Many defense mechanisms in bacteria respond to phage by depleting ATP or NAD (nicotinamide adenine dinucleotide). Both nucleotides are essential for energy metabolism. No energy = no viral replication. And sometimes NAD or ATP depletion causes premature activation of phage lysis machinery 4/

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Sorek Lab @soreklab.bsky.social · 30/07/2025

Nucleotide depletion is a major aspect of antiviral immunity. In humans and bacteria, immune pathways deplete individual deoxy-nucleotides as an antiviral measure. The logic is simple: when the building blocks for making DNA are missing, the virus cannot replicate 3/

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Sorek Lab @soreklab.bsky.social · 14/07/2025

Preprint: “Structural modeling reveals viral proteins that manipulate host immune signaling” Using AI-guided structural modeling, we find new families of viral proteins that sequester or cleave host immune signaling molecules Congrats Nitzan Tal! www.biorxiv.org/content/10.1...

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Sorek Lab @soreklab.bsky.social · 30/04/2025

A beautiful discovery by Joel Tan and Philip Kranzusch, out today in Nature: A DNA-gated molecular guard controls bacterial Hailong anti-phage defence Congrats Joel and Philip! Was a pleasure to contribute to this discovery together with Sarah Melamed www.nature.com/articles/s41...

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Sorek Lab @soreklab.bsky.social · 30/04/2025

Out in Nature today: A new immune signaling molecule, His-ADPR, is produced by defensive TIR domain proteins in bacteria to protect from phage Joint work with the Tamulaitienė and Kranzusch labs www.nature.com/articles/s41... Congrats Carmel Avraham, Dziugas Sabonis, Renee Chang and co-authors!

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Sorek Lab @soreklab.bsky.social · 30/01/2025

Out today @ Science: TIR signaling activates caspase-like immunity in bacteria We report a new immune signaling molecule: N7-cADPR. Produced by phage-induced TIRs and activates a defensive bacterial caspase Congrats Francois Rousset, Ilya Osterman and coauthors! www.science.org/doi/10.1126/...

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Sorek Lab @soreklab.bsky.social · 30/01/2025

Our paper out @Nature: CARD domains mediate anti-phage defense in bacterial gasdermin systems CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems Congrats Tana Wein! Thank you Kranzusch lab! www.nature.com/articles/s41...

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Sorek Lab @soreklab.bsky.social · 23/01/2025

The anti-CBASS protein we found,called Acb3, inhibits diverse bacterial cGAS-like proteins via extensive interactions that include the active site Acb3 also inhibits the activity of human cGAS, binding residues conserved between the human and bacterial homologs 8/10

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Sorek Lab @soreklab.bsky.social · 23/01/2025

Remarkably, we found that Tad4, a phage-encoded anti-Thoeris protein, can also bind and inhibit the plant immune TIR protein BdTIR, as well as the TIR of the human protein SARM1 Conservation of TIRs across bacteria, plants and humans leads to conservation of anti-TIR as well 7/10

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Sorek Lab @soreklab.bsky.social · 23/01/2025

All TIR binders inhibit TIR activity by making direct contacts with the catalytic residue of the TIR active site 6/10

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Sorek Lab @soreklab.bsky.social · 23/01/2025

We found six families of Thoeris inhibitors and one family of cGAS inhibitors, overall encoded in thousands of phages Crystal strx of a complex between Thoeris TIR and one of the inhibitors (thank you Kranzusch lab!) completely matched AF prediction (strx in color; prediction grey) 5/10

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Sorek Lab @soreklab.bsky.social · 23/01/2025

Phage proteins that received high-confidence AF scores for binding an immune protein were tested experimentally - to see if they can inhibit immunity in vivo and in vitro 4/10

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Sorek Lab @soreklab.bsky.social · 23/01/2025

Here, we focused on Thoeris and CBASS, the bacterial immune systems that are the ancestors of eukaryotic TIR and cGAS-STING immunity We clustered 32M phage proteins, selected 38,700 cluster representatives, and used AF to co-fold each of them with bacterial immune proteins 3/10

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Sorek Lab @soreklab.bsky.social · 23/01/2025

Many uncharacterized proteins in the viral protein universe are thought to function in host immune inhibition Using Alphafold (AF), we can now sift through millions of viral proteins for those that bind and inhibit immune proteins 2/10

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Sorek Lab @soreklab.bsky.social · 18/01/2024

Registration for the 2024 Boston Symposium on the Immune System of Bacteria is now open - an exciting program with a fantastic lineup of speakers! Additional talks will be selected from submitted abstracts. Conference website: kranzuschlab.med.harvard.edu/bacterial-im...

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Sorek Lab @soreklab.bsky.social · 04/01/2024

Then, a crystal structure of the ligand-bound effector protein solved the riddle: The molecule was His-ADPR. An amino acid conjugated to a nucleotide – a new class of immune signaling molecules 7/9

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Sorek Lab @soreklab.bsky.social · 04/01/2024

A first hint came when we found a phage protein that inhibits Thoeris by sequestering the molecule. Using this protein as “sponge”, we purified the molecule and sent it to MS/MS. We found fragments that included ADPR, but surprisingly also fragments including histidine 6/9

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Sorek Lab @soreklab.bsky.social · 04/01/2024

At the time, we thought that all bacterial Thoeris systems produce the same gcADPR molecule and work the same way. But now we found a Thoeris system that does not produce gcADPR, so we called it type II Thoeris. What molecule does type II Thoeris produce? 5/9

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Sorek Lab @soreklab.bsky.social · 04/01/2024

At the same time, research in plant immunity showed that plant TIR domains also produce signaling molecules in response to infection. All TIR-derived immune signaling molecules known to date exclusively comprise nucleotides. See the nice fig from the review by Essuman et al 4/9

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Sorek Lab @soreklab.bsky.social · 04/01/2024

Later on, in collaboration with the Kranzusch lab, we found that the signaling molecule is a unique form of cyclic ADP-ribose, which we called 1”-3’ glyco-cyclic ADPR (gcADPR, also called 3'cADPR) 3/9

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Sorek Lab @soreklab.bsky.social · 04/01/2024

In 2018 we discovered that TIR domains are involved in bacterial immunity, and specifically in a defense system called Thoeris (Doron 2018). In this system, a TIR-domain protein senses infection, and then produces a signaling molecule that activates an immune effector 2/9

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Sorek Lab @soreklab.bsky.social · 04/01/2024

A new class of immune signaling molecules generated by TIR domains: histidine conjugated to ADP-ribose Check out our preprint: tinyurl.com/hisADP A fantastic collaboration with the Tamulaitiene and Kranzusch labs

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