Tara Bartolec

Isolation, engineering and ecology of temperate phages from the human gut - Nature Human host-associated cellular products may act as induction agents for bacteriophages.

Very excited to share the latest work from our lab, which was published today in Nature!
nature.com/articles/s41...

PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

Figure 1 from the preprint

Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️

www.biorxiv.org/content/10.1...
#teamtomo

Excited to share our preprint led by Carlos Voogdt et al

We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...

New Preprint from Voogdt et al 👇

Establishes efficient genome-wide transposon mutagenesis & barcode mutant libraries for three Bacteroidales gut bacteria, identifying shared & species-specific essential genes, non-coding elements, & toxin pathways, advancing gut microbiome functional genomics

The functional landscape of the human ubiquitinome Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...

new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...

Happy to see that Spacedust is now published on Nature Methods!
It combines sensitive Foldseek structure search and conserved neighborhood detection to discover functionally-associated gene clusters in prokaryotic & viral genomes.
1/6🧵

Measuring the value and impact of UniProt Case study shows the economic value and impact of UniProt, showing estimated annual gains of up to €5,475 per user.

New impact case study outlines the impressive economic & scientific value of UniProt - the world-leading open data resource for protein sequence & functional information.

Users save up to 219 hours per year, equivalent to net benefits of up to €5,475 per user.

www.ebi.ac.uk/about/news/a...

Excited for New Approaches and Concepts in Microbiology 2025 with sessions on Bacterial systems biology, Bacterial cell biology & protein machines, Microbiomes, Environment & evolution, Pathogenesis & phage, Antibiotic discovery, mechanisms, and resistance. #EESMicrobiology

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"

High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria Systematic mapping of protein-ligand interactions is essential for understanding biological processes and drug mechanisms. Peptide-centric local stability assay (PELSA) is a powerful tool for detectin...

Want to know how the ligands interact with proteins beyond model cell lines, e.g., in tissues or bacteria? Interested in membrane targets? Check out our High-Throughput PELSA method which allows you do all these cool screenings for dozens of ligands within two hours! www.biorxiv.org/content/10.1...

And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣

Jumbo phage killer immune system targets early infection of nucleus-forming phages Jumbo phage killer (Juk) system, a common bacterial immune system in Proteobacteria, recognizes and targets the early phage infection vesicle specific to ϕKZ-like jumbo phages, terminates phage infection, and saves the bacterial cell.

Now online! Jumbo phage killer immune system targets early infection of nucleus-forming phages

Join our favorite microbiology meeting! Fantastic talks, poster sessions, new technologies, and all the hot areas of microbiology in a great environment - experts in cell & systems biology, microbiomes, environment & evolution, pathogenesis, phage & antibiotics
DON’T MISS abstract deadline, April 1

Updated validation reports are now available for structures determined using integrative & hybrid methods (IHM) that extends to structures derived from Crosslinking-MS data, along with previously supported Small Angle Scattering (SAS) data!
⬇️ Read more⬇️
www.wwpdb.org/news/news

🚀 #AlphaFold Database update

AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.

www.ebi.ac.uk/about/news/u...

@pdbeurope.bsky.social

CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d - Nature Microbiology Leveraging RNA-targeting dCas13d enables selective interference with phage protein translation and facilitates measurement of phage gene fitness at a transcriptome-wide scale.

It is finally out!

Muntathar Al-Shimary, @doudna-lab.bsky.social , @cresslab.bsky.social and I present a gene knockdown tool that works in diverse bacteriophages: CRISPRi through antisense RNA Targeting (CRISPRi-ART)!

Check it out @naturemicrobiol.bsky.social
www.nature.com/articles/s41...

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin!
📄 doi.org/10.1093/nsr/...

New version of DefenseFinder available defensefinder.mdmlab.fr (& cli)

Now encompassing 263 systems (+111 this year..!).

Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models

Excited to see this huge piece of work out 🎉 Congrats to everyone involved! If you ever wanted to read a 8in1 paper grab a cup of tea and enjoy 📖

We are very happy to present our work on N-glycoproteomics!🍬 Our method enables the selective enrichment and precise quantification of intact N-glycopeptides to explore the dynamics of glycosylation microheterogeneity.
www.nature.com/articles/s41...

🚨 🧬 Updated preprint on the completed BASEL collection - what's new? Some fun with bacterial immunity and a new P22 relative infecting E. coli K-12. A thread 🧵

Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) ...

Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...

Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) ...

11/11 - Thanks to all involved - what a super collaboration! Savitski lab and @typaslab.bsky.social @embl.org with @alessioyang.bsky.social, @mgalactus.bsky.social / #phage #proteomics #phosphorylation #microbiology #PTMs

10/11 - T7K affected infectivity in nearly half of tested strains! It sometimes even gave >1000-fold advantages to the phage. And none of these strains had Retron-Eco9 or DarTG1, so it is likely that there are many, many more T7K-sensitive systems to be described.

9/11 - So maybe the domesticated K-12 strain (which has lost many defense systems) wasn’t the best model for studying the function of T7K. We assessed this by screening a panel of natural isolates, which harbour a very diverse array of anti-phage defense systems.

8/11 - It seemed so, w/ clear phenotypes for T7K when we armed K-12 w/ plasmids encoding DNA-related defense systems Retron-Eco9 & DarTG1. Both had critical functional residues on their surface, and phosphorylation events deposited by T7K abolished their ability to defend!

7/11 - The stoichiometry results gave us a major clue as to what was really going on - bacterial anti-phage defense systems often work by sensing and/or targeting the phage’s nucleic acids. Perhaps the kinase can brute-force deactivate bacterial defenses?

6/11 - But the T7K gene was reported to be largely dispensable when T7 infected lab strain K-12. Why keep a hyper-promiscuous kinase around if its function is simply to optimise host takeover (translation, transcription)? Doesn’t this activity also hinder T7’s infection cycle?

5/11 - This is achieved through the protein’s C-terminal domain - a long, highly charged and extended alpha-helical region which resembles a histone tail and binds DNA, which colocalises + focuses the loose-canon kinase’s activity towards nucleic acid-binding proteins.

4/11 - But how do you interpret a kinase’s role if it phosphorylates EVERYTHING? We tried estimating phosphorylation stoichiometry and found that there was some order to the madness - nucleic-acid binding proteins were much more heavily modified than the rest of the proteome.