Uday Tak

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...

NEW Review from @soreklab.bsky.social @dinahoch.bsky.social explains how immune pathways manipulate the availability of nucleotides, chemically modify nucleotides to generate immune signalling molecules, and produce altered nucleotides that poison viral replication
#immunosky #microsky #phagesky

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...

RNA N-glycosylation enables immune evasion and homeostatic efferocytosis - Nature N-glycans on glycoRNAs prevent innate immune sensing of endogenous small RNAs, and the natural mechanism they use demonstrates how glycoRNAs exist on the cell surface and in the endosomal network with...

#GlycoPower! @vijayrathinam.bsky.social
@raflynn5.bsky.social @vinnieviruses.bsky.social &co show @nature.com that N-glycosylation of host small-RNAs present at cell surface prevents immune recognition by TLR3 and TLR7 upon apoptotic cells uptake avoiding autoinflammation!

Kiwa is a membrane-embedded defense supercomplex activated at phage attachment sites Zhang, Todeschini, and Wu et al. show that the bacterial defense system Kiwa senses phage attachment at the membrane and assembles a transmembrane complex that halts infection by blocking phage DNA re...

Thrilled to see our Kiwa story out today! A membrane-associated supercomplex that senses infection and blocks replication and transcription.

www.cell.com/cell/fulltex...

Huge congratulations to Yi and Zhiying for bringing it home, to Thomas for starting us off, and to all the collaborators.

1/16 New pre-print from the Sternberg Lab!
We uncover how temperate phages can use RNA-guided transcription factors to remodel the flagellar composition of their bacterial host and enhance their fitness.
Find the preprint and full story here: tinyurl.com/mshwjd77

🦠🧍‍♀️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/...

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...

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...

Our new work understanding how phages are detected by the bacterial immune system is posted on bioRxiv! Check out Toni’s thread for a synopsis👇

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco

PhD Project: Discovering Novel Mechanisms of Phage Genome Evolution We are looking for an awesome PhD student to join our research team to investigate how bacteriophages (phages) generate targeted mutations that enable them to evolve and infect new bacterial hosts. Yo...

PhD opportunities at @flindersuniversity.bsky.social in Adelaide, Australia's most liveable city, to study genetics in #phage

We will also have genetics #postdoc positions too!

#microsky #phagesky

www.linkedin.com/pulse/phd-pr...

Functional amyloid proteins confer defence against predatory bacteria Nature - Escherichia coli uses curli fibres, oligomers of the functional amyloid CsgA, as a barrier to protect against the predatory bacteria Bdellovibrio bacteriovorus and Myxococcus xanthus in a...

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/.

Phage arabinosyl-hydroxy-cytosine DNA modifications result in distinct evasion and sensitivity responses to phage defense systems Mahler et al. describe a phage DNA modification that adds arabinose to cytosines via a hydroxy linkage. This 5ara-hC modification can be further modified to double and triple arabinosylation by phage-...

Phage DNA modifications evade defense

Phage DNA modification adds arabinose to cytosines via hydroxy linkage (5ara-hC) w/ potential double & triple arabinosylation. Arabinosylated phages are protected from DNA-targeting CRISPR-Cas & restriction modification
www.cell.com/cell-host-mi...

Extremely excited to share I have accepted an offer to be an Assistant Professor in the MCDB department at the University of Michigan! Go Blue! The Ledvina lab will investigate the molecular interworking of the bacterial immune systems including defense against both viral and bacterial pathogens.

Structural basis of BAX pore formation @science.org
www.science.org/doi/10.1126/...

Looking for a deep dive into 2D classification in #cryoEM?

These recent guide pages cover practical aspects & parameter choices when running these jobs in #CryoSPARC, along with the theory behind expectation maximization: guide.cryosparc.com/processing-d... and guide.cryosparc.com/expectation-...

The June issue is live nature.com/nbt/volumes/...

On the cover, Khan et al. present a molecular census of retrons, performing the same battery of tests across many distinct systems to identify similarities and differences go.nature.com/3MOsMBx

Exciting fundamental discovery!

Early embryos fight bacteria WITHOUT immune cells

Zebrafish, mouse, and human embryos use epithelial cells (trophoectoderm)—not immune cells—to engulf and destroy 𝘌. 𝘤𝘰𝘭𝘪 and 𝘚. 𝘢𝘶𝘳𝘦𝘶𝘴

Hoijman Lab Barcelona 🇪🇸
𝘊𝘦𝘭𝘭 𝘏𝘰𝘴𝘵 𝘔𝘪𝘤𝘳𝘰𝘣𝘦

www.sciencedirect.com/science/arti...

ProtPhage: a deep learning framework for phage viral protein identification and functional annotation. #PhageProteins #FunctionalAnnotation #DeepLearning #Phages #Bioinformatics 🧬 🖥️
academic.oup.com/bib/article/...

1/10 New pre-print(s) from the Sternberg Lab in collaboration with Leifu Chang's Lab! We uncover the unprecedented molecular mechanism of CRISPR-Cas12f-like proteins, which drive RNA-guided transcription independently of canonical promoter motifs.
Full story here:
www.biorxiv.org/content/10.1...

Elucidating the mechanisms of action and evolutionary history of phage anti-defence proteins Phages and bacteria are locked in a molecular arms race, with phage anti-defence proteins (ADPs) enabling them to evade bacterial immune systems. To streamline access to information on ADPs, we develo...

Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at ‪EMBL-EBI (@ebi.embl.org)‬
and the University of Cambridge (@cam.ac.uk‬)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"

New research reveals the mode of action of the Pseudomonas aeruginosa #T6SS Tse4 toxin. Tse4 forms ion-selective, voltage-sensitive channels in bacterial membranes, coupling cell depolarization with K⁺ efflux. This highlights a key antibacterial strategy. #PFPsky
doi.org/10.1371/jour...

Check out this excellent study led by Amy Conte and Aaron Whiteley on how bacterial NLR-like proteins sense infection by RNA phages! Congrats to the team @amyconte.bsky.social, @aaronwhiteley.bsky.social

Phage people: Rich Losick and I are combing the world looking for T4 rIIB mutant FC0 (also known as P13). FC0 was the starting point for Francis Crick's beautiful 1961 paper on the triplet nature of the genetic code. We want to sequence it. Anyone have it in an ancient stock collection?

Check out our latest preprint! We show that the same antibacterial toxin requires different immunity proteins depending whether it’s intra or extracellular

We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.

Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.

cryotud.github.io/locscale/

Really excited to share our resource and analysis of AlphaFold-predicted monomers and homodimers across viruses and phages. Project driven by fab PhD student @rodai.bsky.social and with our great collaborators Joana Pereira @joanampereira.bsky.social and @ninjani.bsky.social

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!

1/10 Today in @science.org in collaboration with
the Liu group we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells. drive.google.com/file/d/1I-Ub...

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