Amar Deep
amardeeep.bsky.social
Amar Deep
@amardeeep.bsky.social
Structural biologist interested in microbial defense and anti-defense strategies!

https://scholar.google.com/citations?hl=en&user=PkTFTiQAAAAJ
Reposted by Amar Deep
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Reposted by Amar Deep
You’ve heard of ubiquitination, meet deazaguanylation: Doug Wassarman in our lab discovered phage defense pathways have co-opted Q nucleobase biosynthetic enzymes to catalyze a new form of protein conjugation chemistry @science.org

www.science.org/doi/10.1126/...
September 25, 2025 at 7:16 PM
Another important contribution from Sorek and Blokesch labs.

This engineering strategy with synthetic inhibitors could yield more powerful phages than natural inhibitors, since the latter sometimes trigger other defense systems..
Preprint: De-novo design of proteins that inhibit bacterial defenses

Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications

Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
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...
www.biorxiv.org
September 4, 2025 at 7:01 AM
Reposted by Amar Deep
The beautiful, ever-expanding universe of viral proteins targeting nucleotide immune signals!

Paper by @reneechang.bsky.social in @cp-molcell.bsky.social on a nucleotide sponge www.cell.com/molecular-ce...

and preprint by @doudna-lab.bsky.social on viral nucleases www.biorxiv.org/content/10.1...
A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti-phage defense
Chang et al. discover anti-CBASS 4 (Acb4), a family of viral sponges that inhibits bacterial immunity by sequestering nucleotide immune signals. Acb4 homologs in phages that infect hosts across all ma...
www.cell.com
August 22, 2025 at 9:02 PM
Reposted by Amar Deep
A widespread family of viral sponge proteins reveals specific inhibition of nucleotide signals in anti- #phage defense

www.cell.com/molecular-ce... #bacteriophage #MicroSky
August 22, 2025 at 9:21 AM
Reposted by Amar Deep
We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology

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

Was fun to write this piece with Dina Hochhauser!

Here is a thread to explain the premises

1/
Manipulation of the nucleotide pool in human, bacterial and plant immunity - Nature Reviews Immunology
Modification of the nucleotide pool is emerging as key to innate immunity in animals, plants and bacteria. This Review explains how immune pathways conserved from bacteria to humans manipulate the nuc...
www.nature.com
July 30, 2025 at 6:05 AM
Reposted by Amar Deep
🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

www.science.org/doi/10.1126/...
www.science.org
July 24, 2025 at 6:23 PM
Reposted by Amar Deep
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...
July 14, 2025 at 7:36 AM
Excellent study, led by @hannahledvina.bsky.social from the Whiteley lab @aaronwhiteley.bsky.social
Check out our new study on how bacteria defend themselves against a peculiar clade of organisms – predatory bacteria! This work was a monumental effort led by @hannahledvina.bsky.social (see her excellent summary👇). The bacterial immune system continues to amaze me...
Words cannot describe how excited I am to share the findings from the second half of my postdoc in @aaronwhiteley.bsky.social's lab where we discover that bacteria use functional amyloids to defend themselves from predatory bacteria. rdcu.be/euu5Y. See thread for details on this epic adventure 1/.
July 3, 2025 at 2:19 PM
Reposted by Amar Deep
We are all somatic mutation mosaics.
"There are trillions of cells in a human body and so the total number of somatic mutations acquired in a single individual may well exceed quadrillions, millions of times the size of the human genome."
@nature.com
nature.com/articles/s41...
The Somatic Mosaicism across Human Tissues Network - Nature
The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.
nature.com
July 2, 2025 at 4:21 PM
Reposted by Amar Deep
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!
June 4, 2025 at 1:45 PM
Reposted by Amar Deep
Exciting news!! Our latest paper is out in Nat. Microbiol. @natmicrobiol.nature.com

We show that a sub-lineage of 7th pandemic V. cholerae has acquired mobile genetic elements packed with phage defense systems—rendering it multi-phage resistant 😳 ..... 1/3

www.nature.com/articles/s41...
West African–South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems - Nature Microbiology
The West African–South American lineage of Vibrio cholerae contains multiple distinct anti-phage defence systems that provide resistance to various phage families, including vibriophage ICP1, a key pr...
www.nature.com
May 22, 2025 at 6:14 PM
Reposted by Amar Deep
I will be recruiting new postdocs with start dates end 2025 - early 2026. If you'd like to work at the Pasteur Institute in the heart of Paris surrounded by amazing scientists, reach out to discuss possible projects on SynBio / Bacterial Immunity!
May 18, 2025 at 3:20 PM
Reposted by Amar Deep
📜 Bacterial community-emitted volatiles regulate Arabidopsis growth and root architecture in a distinct manner from those from individual strains

🧑‍🔬 @gozdemerveturksoy.bsky.social, @tonnigrubeandersen.bsky.social, Stanislav Kopriva, et al.

📔 @mplantpcom.bsky.social

#️⃣ #PlantScience #PlantImmunity
Bacterial community-emitted volatiles regulate Arabidopsis growth and root architecture in a distinct manner from those from individual strains
Short summary: This study reveals that the effects of bacterial community-produced volatiles on Arabidopsis growth and root architecture are an emergent property beyond the sum of effects by individua...
www.cell.com
May 12, 2025 at 11:10 AM
Reposted by Amar Deep
Our paper on how integrons are biobanks of novel minimal defense systems is now out www.science.org/doi/10.1126/... Two main conclusions on this excellent work led by @eloilittner.bsky.social @baptistedarracq.bsky.social 1/n
May 9, 2025 at 1:07 PM
Reposted by Amar Deep
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...
April 30, 2025 at 6:59 PM
Reposted by Amar Deep
Check out our review on "PLK4: Master Regulator of Centriole Duplication and Its Therapeutic Potential".

Everything you need to know about centriole duplication, mitotic stopwatch and TRIM37-mediated cancer-specific vulnerabilities.

onlinelibrary.wiley.com/doi/10.1002/...
PLK4: Master Regulator of Centriole Duplication and Its Therapeutic Potential
Centrosomes catalyze the assembly of a microtubule-based bipolar spindle, essential for the precise chromosome segregation during cell division. At the center of this process lies Polo-Like Kinase 4 ...
onlinelibrary.wiley.com
April 27, 2025 at 8:09 AM
Reposted by Amar Deep
In this first publication from the lab, now out in @narjournal.bsky.social, we review the current state of RNA phage biology with a focus on meta-omics methods. Many things left to be discovered!

#PhageSky

doi.org/10.1093/nar/...
Advancing RNA phage biology through meta-omics
Abstract. Bacteriophages with RNA genomes are among the simplest biological entities on Earth. Since their discovery in the 1960s, they have been used as i
doi.org
April 23, 2025 at 9:04 AM
Reposted by Amar Deep
Check out our new story led by @aesully98.bsky.social describing how bacteria turn immune evasion against phage! In collaboration with @benmorehouse.bsky.social lab, we discover that bacteria guard their nucleotide second messenger pool using a nucleotidyltransferase related to Cas10/CRISPR enzymes
April 8, 2025 at 2:52 AM
Reposted by Amar Deep
Deazaguanylation is a nucleobase-protein conjugation required for type IV CBASS immunity https://www.biorxiv.org/content/10.1101/2025.04.06.647259v1
April 7, 2025 at 5:17 AM
Reposted by Amar Deep
#NewComicAlert!
We are back with another inspiring comic with Tinkle Magazine featuring cognitive and behavioural neuroscientist Dr Abhilasha Joshi! 🧠 🐀

Happy reading!
Download your free copy here: bit.ly/ncbsxtinklec...

@rhythmicspikes.bsky.social

#sciencecomics #womenscientists
April 4, 2025 at 12:31 PM
Reposted by Amar Deep
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!
March 31, 2025 at 10:05 PM
Reposted by Amar Deep
biorxiv.org/content/10.1...
We found ubiquitous recombinases from cryptic prophages may invert DNA to form new, chimeric proteins that inhibit phages by blocking adsorption. Congratulations to Joy, Daniel, Rodolfo and Michael for their strong efforts.
Serine Recombinase PinR Inverts Cryptic Prophage DNA to Block Adsorption of Phages
Recombinases catalyze site-specific integration, excision, and inversion of DNA and are found in myriad defense islands; however, their function in phage-defense is unknown as they are frequently dism...
biorxiv.org
March 29, 2025 at 7:46 AM
Reposted by Amar Deep
Interrupting your regularly scheduled doom scrolling for some cool science by my awesome colleagues www.cell.com/cell-host-mi...
Sequential membrane- and protein-bound organelles compartmentalize genomes during phage infection
The pre-nuclear stage of Chimalliviridae infection and whether the phage nucleus is essential have remained mysterious. Armbruster and Rani et al. demonstrate that the phage nucleus is required for ph...
www.cell.com
March 31, 2025 at 6:38 PM
Reposted by Amar Deep
🧪🧪🧪10 incredible findings about Cas10-relative, mCpol:
result number 10 will surprise you!🧪🧪🧪

@erinedoherty.bsky.social and I teamed up to understand the role and function of Cas10-relative, mCpol, and its role in antiphage immunity. For more, check out Erin's thread 👇
Preprint alert! ✨ In this project that I co-led with @benadler.bsky.social, we show that a miniature CRISPR-Cas10-like enzyme, mCpol, uses a novel inverse signaling mechanism to prevent the spread of viruses that attempt immune evasion by depleting host cyclic nucleotides.

Check it out:
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...
www.biorxiv.org
March 31, 2025 at 5:31 PM