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Reposted by Tara Bartolec

Ruoshi @ruoshiz.bsky.social · 22d

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.
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Nature Methods @natmethods.nature.com · 22d

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social

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

De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods

This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

www.nature.com

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Reposted by Tara Bartolec

EMBL-EBI @ebi.embl.org · Jun 25

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...

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.

www.ebi.ac.uk

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Reposted by Tara Bartolec

Typas Lab @typaslab.bsky.social · Jun 23

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

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Reposted by Tara Bartolec

Khalimat Murtazalieva @khalimat.bsky.social · Jun 8

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"

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...

www.biorxiv.org

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Reposted by Tara Bartolec

Savitski Lab @savitski-lab.bsky.social · Apr 29

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...

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...

www.biorxiv.org

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Reposted by Tara Bartolec

Alexander Harms @aharms485.bsky.social · Apr 8

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

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Cell - a Cell Press journal @cp-cell.bsky.social · Mar 19

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

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.

dlvr.it

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Reposted by Tara Bartolec

Typas Lab @typaslab.bsky.social · Mar 26

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

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Reposted by Tara Bartolec

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Mar 11

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

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Reposted by Tara Bartolec

EMBL-EBI @ebi.embl.org · Mar 3

🚀 #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

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Reposted by Tara Bartolec

Ben Adler @benadler.bsky.social · Feb 26

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...

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.

www.nature.com

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Reposted by Tara Bartolec

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · Feb 22

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/...

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Reposted by Tara Bartolec

Aude Bernheim @audeber.bsky.social · Feb 19

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

Webservice | DefenseFinder webservice and knowledge base

On this site, you can freely use (without any login) the DefenseFinder webservice (see below) and get help to navigate the ever expanding world of defense systems.There is a collaborative knowledge ba...

defensefinder.mdmlab.fr

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Reposted by Tara Bartolec

miraburtscher.bsky.social @miraburtscher.bsky.social · Feb 10

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 📖

Savitski Lab @savitski-lab.bsky.social · Feb 10

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...

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Reposted by Tara Bartolec

Savitski Lab @savitski-lab.bsky.social · Feb 10

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...

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Reposted by Tara Bartolec

Alexander Harms @aharms485.bsky.social · Feb 6

🚨 🧬 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 🧵

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Typas Lab @typaslab.bsky.social · Dec 23

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) ...

www.biorxiv.org

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Tara Bartolec @tarabartolec.bsky.social · Dec 23

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

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) ...

www.biorxiv.org

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Tara Bartolec @tarabartolec.bsky.social · Dec 23

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.

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Tara Bartolec @tarabartolec.bsky.social · Dec 23

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.

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Tara Bartolec @tarabartolec.bsky.social · Dec 23

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!

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Tara Bartolec @tarabartolec.bsky.social · Dec 23

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?

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Tara Bartolec @tarabartolec.bsky.social · Dec 23

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?

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Tara Bartolec @tarabartolec.bsky.social · Dec 23

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.

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Tara Bartolec @tarabartolec.bsky.social · Dec 23

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.

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