Tara Bartolec

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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.

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@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.

3/11 - T7 infection induced a massive wave of phosphorylation - dependent on T7K! We found that T7K is incredibly promiscuous, exceeding the combined activity of 500+ human kinases in just 5 min! Promiscuity is likely through dual-specificity (S/T & Y) + no sequence motif.

2/11 - T7K has been studied since the 70s w/ a handful of (v. abundant) substrates identified using traditional biochem (SDS-PAGE, radio-labelling, WBs). We studied T7 w/ modern bacterial phosphoproteomics (better sensitivity + specificity) and found a COMPLETELY different story…

1/11 - With Karin Mitosch and Clément Potel + colleagues in Savitski lab and @typaslab.bsky.social @embl.org, I’m very happy to share our discovery of a hyper-promiscuous phage protein kinase (T7K) which broadly deactivates bacterial defenses! 🦠
www.biorxiv.org/content/10.1...

You have to believe you can write a manuscript in a week, so that it will end up only taking three months.

YouTube video by WEHImovies DNA Break Repair by Homologous Recombination (2024) Drew Berry wehi.tv

Delighted to publish my new molecular animation:

DNA Break Repair by Homologous Recombination

youtu.be/Xe-83tBcxhs

The disciplinary matrix of holobiont biology Uniting life’s seen and unseen realms guides a conceptual advance in research

The holobiont is more than just corals, and has spin off terms (can you say holoproteome? better than metaproteome imo). Makes sense and actually love the term is going places. (Michelle Heck, not here yet, just share this paper with me)
#proteomics

www.science.org/doi/10.1126/...