Mart Krupovic

Fresh from our group, a new role for oxygen production in ammonia-oxidizing archaea:

Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea

Congrats to Thomas Pribasnig for this great work!

Check it out here:
www.biorxiv.org/content/10.6...

Preprint: Systematic discovery of TIR-based immune signaling systems in bacteria

Conservation of TIR-derived signals accross the tree of life! We found bacterial TIR immune systems that signal via canonical cADPR (like in humans) and 2'cADPR (a plant immune signal).

Documented 11 Thoeris types

Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st

🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...

Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism The emergence of cell compartmentalization depends on membrane fission to create the endomembrane compartments. In eukaryotes, membrane fission is commonly executed by ESCRT-III, a protein complex con...

New preprint from the lab!!🎉
We show that Asgard archaea ESCRT-III proteins can trigger membrane fission and reveal its molecular mechanism, offering clues to how these cells may have built internal compartments. But do these organisms even have these compartments?
www.biorxiv.org/content/10.1...

Explicit description of viral capsid subunit shapes by unfolding dihedrons - Communications Biology A proposed geometric framework describes and classifies all possible protein subunit shapes in viral capsids through spherical tiling theory, revealing different interaction patterns based on subunit ...

Explicit description of viral capsid subunit shapes by unfolding dihedrons by Ryuya Toyooka et al. www.nature.com/articles/s42...

Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses - Nature Communications Borgs are large extrachromosomal elements of anaerobic methane-oxidizing archaea. Here, via in silico protein structure prediction of ~10,000 Borg proteins, the authors reveal that Borgs share numerou...

Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses

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

@luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social

Congrats to all coauthors, @sonaida.bsky.social, Ulysse Guyet, @tomdelmont.bsky.social, Eugene Koonin, et al. @pasteur.fr @cnrs.fr

Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.

Check out our latest paper on mirusviruses, one of the most remarkable new groups of protist viruses - extremely diverse, carry lots of spliceosomal introns (including new homing introns) and are at the evolutionary crossroads between tailed phages and herpesviruses! www.nature.com/articles/s41...

Intron-rich viruses - WOW!
rdcu.be/eSfG2

Widespread and intron-rich mirusviruses are predicted to reproduce in nuclei of unicellular eukaryotes - Nature Microbiology Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.

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

Thrilled to share our new study! We show that mirusviruses include lineages packed with spliceosomal introns and likely replicating in the nucleus of unicellular eukaryotes—a sharp contrast to most large and giant eukaryotic viruses that replicate in the cytoplasm.

New update for the gbdraw web app!🚀
You can now display gene labels ONLY on the first genome in the linear diagram. Just select "First" in the "Label layout" option.
Try it out here👉: gbdraw.streamlit.app
#gbdraw #bioinformatics #genomics #visualization #virology #microbiology #streamlit

Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins www.biorxiv.org/content/10.1...

Recently out: “Uniform dynamics of cohesin-mediated loop extrusion in living human cells”. In this study led by brilliant former PhD student Thomas Sabaté we use live cell microscopy and polymer simulations to characterize how DNA loops and TADs form in human cells by cohesin-driven extrusion. (1/4)

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages.

Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms.

A thread 1/8

Cryo-EM reveals open and closed Asgard chromatin assemblies Ranawat et al. show the cryo-EM structures of Asgard archaeal chromatin assemblies, revealing that the histone HHoB assembles into both compact closed and extended open hypernucleosomes. The closed co...

Let’s wrap things up: my commentary on the Asgard hypernucleosomes.

Congratulations to all the authors of the paper 🍾!

kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...

Cryo-EM reveals open and closed Asgard chromatin assemblies: Molecular Cell www.cell.com/molecular-ce...

YouTube video by Archaeal Adventures Nested Symbiosis in Extreme Environments

New video on Nested Symbiosis in extreme environments out on my YouTube Channel. Give it a watch if you can, a great paper by @mkrupovic.bsky.social

Original Paper: doi.org/10.1038/s415...

youtu.be/OQR5obtf7-4

Version 2 is out! More comprehensive text plus new tissue- and pathway-specific analysis revealing how different viruses trigger systemic aging through diverse mechanisms.
www.biorxiv.org/content/10.1...

Amazing piece of work from @rtoshiro.bsky.social
& Kim Seed at UC Berkeley. 🙌
Played a tiny role in this work.

Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses

www.biorxiv.org/content/10.1...

Welcome to @pasteur.fr , Spyros! It will be great to have you!

My lab is recruiting a post-doc ! please share ! emploi.cnrs.fr/Offres/CDD/U...

Thanks Karim.

Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...

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

the sun is shining through the clouds in the sky above the ocean ALT: the sun is shining through the clouds in the sky above the ocean

Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis www.nature.com/articles/s41...
this project was led by @omernadel.bsky.social and is a joint work between the labs of @bejalab.bsky.social, Debbie Lindell and Oded Kleifeld from @biologytechnion.bsky.social

Preprint: Bacteria sense virus-induced genome degradation via methylated mononucleotides

tinyurl.com/ch3damp

We show how molecular byproducts released during virus-induced cell exploitation are used as signals to trigger host immunity

Revealed by the amazing Ilya Osterman. See his thread below👇

A Bundled Antiparallel Cytochrome Nanowire Structure Suggests Roles in Cell-Cell Electron Transfer and Biofilm Formation Long-range extracellular electron transfer enables respiring microbes to use minerals, other organisms, or electrodes as electron acceptors by transporting electrons microns away from the cell surface...

Check out the fancy anti-parallel cytochrome nanowire bundles structure we've solved. This structure originates from a bacterium, strain name WTL (well-to-live), isolated by the Bond group from the Soudan Underground Iron Mine, located 713 m below the surface. www.biorxiv.org/content/10.1...

Methanobrevibacter smithii

Curious about the top methane-maker in your gut? Meet this month's featured microbe and find out! 🦠💨🔥 in @cp-trendsmicrobiol.bsky.social #archaeasky
@sgribaldo.bsky.social @pasteur.fr
🔗 Full article linked in reply👇
www.sciencedirect.com/science/arti...

This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com

rdcu.be/eLtCH

Applications closing tonight (midnight French time) !!!
Still a few hours to apply !!

APPEL A PROJET

📣 PhD Scholarship Opportunity for International Students!
Are you looking to do a PhD in soil microbial and viral ecology?
✍️ Get in touch now!!
✅ Requirements: Masters degree, Distinguished CV, Highly motivated
⏳ Application deadline: November 24
www.univ-lyon1.fr/recherche/fo...

Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️
Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...