Ashley Sullivan

A new preprint led by Sonomi Yamaguchi in our lab describes a bacterial anti-phage defense system named Clover that uses nucleotide signals to both activate and inhibit host immunity.

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

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...

Identifying phage proteins that activate the bacterial innate immune system Bacteria have evolved sophisticated antiphage systems that halt phage replication upon detecting specific phage triggers. Identifying phage triggers is crucial to our understanding of immune signaling...

I am delighted to share that my work in the @aaronwhiteley.bsky.social lab is now on bioRxiv! We used a large-scale genetic screen to begin defining the vast landscape of phage proteins that trigger immune signaling in bacteria.
www.biorxiv.org/content/10.1...

Excited to share that my work in the @aaronwhiteley.bsky.social lab describing chaperone-mediated phage sensing by a bacterial NLR-related protein is out in @plosbiology.org!

CBASS, CRISPR, and mCpol- oh my! What a satisfying collaboration with @aaronwhiteley.bsky.social 's lab- we uncovered a new cyclic dinucleotide signaling pathway, but it doesn't work how you'd expect! Check out the thread from @aesully98.bsky.social for an overview of the most important findings!

A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signaling that share mechanistic features with human anti-viral systems. In these pathways, including CBASS a...

Also—check out the complementary work led by @erinedoherty.bsky.social and @benadler.bsky.social in @doudna-lab.bsky.social lab that just went up on bioRxiv!

Huge shout-out to all of the authors from the @aaronwhiteley.bsky.social and @benmorehouse.bsky.social labs that were so instrumental to this project! A special thank you to our collaborators L. Aravind and Max Burroughs for their incredible bioinformatic analyses!

In total, we uncovered a novel mechanism of immune evasion sensing in bacteria. The Panoptes system is part of a “layered” immune system that flips the liability of a nucleotide-derived second messenger in immune signaling against the phage, adding an interesting dimension to phage-bacteria warfare.

Finally, we wanted to explore the relationship between CBASS and Panoptes, given the importance of Acb2 in both nucleotide-based signaling systems. We found that 53% of all Panoptes systems co-occur with CBASS, suggesting that Panoptes systems are predominantly guardians of CBASS in bacteria.

Consistent with this, we found that OptE robustly inhibited bacterial growth unless an OptS-derived nucleotide was present and that OptS constitutively synthesizes 2′,3′-c-di-AMP in vivo in the absence of phage infection.

These data led us to hypothesize that OptS-synthesized nucleotides were actually inhibiting, rather than activating, the OptE effector. Upon phage infection, however, Acb2 sequesters the OptS product away from OptE, unleashing its growth inhibition effect.

These findings left us puzzled: How does the Acb2 nucleotide sponge protein activate the Panoptes system? Based on its ability to bind diverse nucleotide products, we proposed that Acb2 also binds the product of OptS (2′,3′-c-di-AMP), which is exactly what we found.

Acb2 was recently discovered by the Bondy-Denomy and Chen Labs to be an anti-defense protein that acts as a nucleotide “sponge,” sequestering CBASS-derived cyclic oligonucleotide signaling molecules.

Intriguingly, the escaper phages we identified encoded loss-of-function mutations exclusively in the anti-CBASS 2 (acb2) gene. Consistent with this, we found that acb2 was necessary and sufficient to activate Panoptes defense.

We now knew that nucleotide signaling was a key component of the Panoptes system, but we were left wondering: how does the phage activate defense? To answer this question, we turned to phages that were able to escape Panoptes.

We tested the activity of OptS by incubating it with a range of NTPs and found that it used ATP as a substrate to specifically produce 2′,3′-c-di-AMP, an isomer of c-di-AMP. We used a series of phosphodiesterases to show that the linkage included a 3′–5′ and 2′–5′ bond.

To better understand the mechanism of this system, we determined a crystal structure of OptS and found that it resembled the catalytic regions of both Cas10 and GGDEF enzymes and formed a stable tetrameric complex.

We first explored the antiphage activity of Panoptes and found that it robustly and specifically defended against Teven phages from the Straboviridae family.

Nucleotide-based signaling is a hallmark of many antiphage systems (CBASS, Pycsar, Thoeris, etc.). Here we investigated Panoptes, a two-gene operon (optSE) that we predicted would similarly use nucleotide second messengers to carry out an immune response.

A minimal CRISPR polymerase produces decoy cyclic nucleotides to detect phage anti-defense proteins Bacteria use antiphage systems to combat phages, their ubiquitous competitors, and evolve new defenses through repeated reshuffling of basic functional units into novel reformulations. A common theme ...

Excited to share that my work from the @aaronwhiteley.bsky.social lab is now on bioRxiv! With @benmorehouse.bsky.social, we discovered that the Panoptes defense system—named after the all-seeing watchman of Hera—uses decoy nucleotides to detect phage anti-defense proteins.

Update: They were removed from our reviewer assignments completely. I'm so sorry to all those graduate students. Anonymous to protect the identity of the NIH employee I spoke to...I am on study section next month to discuss F awards. We were just instructed to put the F31-Diversity applications on the bottom of our priority list for review because there is a chance we may not be able to review them. My heart is breaking for the grad students and their mentors that put so much work into these just for them to be disqualified and thrown out.

Just in case you thought that removing DEI criteria would mean that everyone is competing equally: NIH is removing grad students from underrepresented backgrounds from the applicant pool altogether. Their applications will not be considered. Other students, not from these backgrounds, will be.

A bacterial NLR-related protein recognizes multiple unrelated phage triggers to sense infection Immune systems must rapidly sense viral infections to initiate antiviral signaling and protect the host. Bacteria encode >100 distinct viral (phage) defense systems and each has evolved to sense cruci...

I’m so excited to share that some of my grad work in the @aaronwhiteley lab is now available on bioRxiv! We used an AlphaFold-multimer screen to uncover how a bacterial NLR-related proteins senses multiple phage-encoded proteins to confer phage protection. Link: www.biorxiv.org/content/10.1...

Our review comparing bacterial and eukaryotic immune systems is out now. Check out Hannah’s thread for the highlights!

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