Mart Krupovic

Very proud of the work from lab members and collaborators that coincidentally came out today www.pnas.org/doi/10.1073/... and www.nature.com/articles/s41.... A bacterial and viral pathogen associated with mass mortality in seastars and oysters. @kevinzhong2006.bsky.social @rhizalyssa.bsky.social

A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans www.biorxiv.org/content/10.1...

Tat-dependent bundling pilus of a halophilic archaeon assembles by a strand donation mechanism and facilitates biofilm formation
#microbiology #archaea #biofilm
@pnas.org
www.pnas.org/doi/10.1073/...

Novel viruses of Haloquadratum walsbyi expand the known archaeal virosphere of hypersaline environments Abstract. Solar salterns represent unique systems with low diversity microbial communities that serve as an excellent model for studying the evolution and

Check out the new paper of my former lab about novel haloviruses infecting Haloquadratum walsbyi, the "square queen archaeon" of hypersaline systems 👑🟪
academic.oup.com/ismej/advanc...

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...

We wrote a review on the free nucleotide pool as a central playground in human, bacterial, and plant immunity – now out in Nature Reviews in Immunology

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

Was fun to write this piece with Dina Hochhauser!

Here is a thread to explain the premises

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Cell surface differences within the genus Methanosarcina shape interactions with the extracellular environment | Journal of Bacteriology Methanogenic archaea, including Methanosarcina, play crucial roles in biotechnology and climate processes, impacting wastewater treatment, carbon capture, and greenhouse gas emissions. Methanosarcina ...

The latest minireview from my lab, “Cell‑surface differences within the genus Methanosarcina shape interactions with the extracellular environment,” is now online in the Journal of Bacteriology. Read the open‑access article here: journals.asm.org/doi/10.1128/....

Tn7 family transposons that include all of the guide RNA-directed transposons (CAST) are common in bacteria. We now find diverse representatives across archaea, with many in the Asgard group. Reviving an Asgard element confirmed the exciting behaviors of the family #MicroSky #TESky

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.

🚨 FIRST PAPER ALERT 🚨

My first research paper I've been involved with is out now as a preprint 🦠🥳🦠

#archaea #microsky #PhD

A dinoflagellate-infecting giant virus with a micron-length tail Viral infection is a ubiquitous source of marine plankton mortality, but relatively few viruses that infect phytoplankton have been characterized. Here we describe a virus, PelV-1, with unusual morpho...

Excited that this is out as a preprint! ❇️

We are introducing a novel dinoflagellate giant virus that holds so many mysteries!

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

graphical abstract of the article the extended mobility of plasmids

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

And the story is published now!🍾
www.nature.com/articles/s41...

Open access link: rdcu.be/exnOc

Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social

Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

A dinoflagellate-infecting giant virus with a micron-length tail Viral infection is a ubiquitous source of marine plankton mortality, but relatively few viruses that infect phytoplankton have been characterized. Here we describe a virus, PelV-1, with unusual morphological and genomic features that infects a dinoflagellate, Pelagodinium sp. Both host and virus were isolated from the epipelagic zone in the North Pacific Subtropical Gyre. PelV-1 has a ~200 nm capsid size, and the virion variably exhibits two appendages, the presence and length of which may reflect different stages of virion maturity or artifacts of sample preparation. The appendages are a thinner 30 nm-wide tail-like structure that can extend to 2.3 µm — the longest virus appendage described to date — and a shorter, thicker (>40-70 nm) protrusion, which appears to emerge from a star-shaped capsid opening directly opposite the attachment point of the long, thin tail. Sequencing and assembly of material in a purified lysate generated a high-coverage (> 4,000x) genome of 459 kb (33.8% GC). A second, distinct genome of 504 kb (25.8% GC) was also assembled, but had low read coverage (< 24x), suggesting the presence of a low-abundance, co-cultured virus (co-PelV). Phylogenetic analysis indicates that both PelV-1 and co-PelV are members of Mesomimiviridae. They contain various genes for the metabolism of amino acids (e.g., asparagine synthase), carbohydrates (e.g., epimerase, glycosyl hydrolase, aconitate hydratase, succinate dehydrogenase of the TCA cycle), and lipids (e.g., phospholipases), as well as other noteworthy genes (e.g., light-harvesting complex, rhodopsin, ion channel, sugar transporters, aquaporin). PelV-1 also has ORFs most similar to tail fiber genes of Synechococcus phage and other tail domain-containing protein homologs. The ecological advantages that might be conferred by the extraordinarily long tail and metabolic genes of PelV-1 is unknown, but this isolate expands the scope of morphological and metabolic diversity of viruses and suggests many more unusual marine viruses await discovery. ### Competing Interest Statement The authors have declared no competing interest. National Science Foundation, https://ror.org/021nxhr62, OIA #1736030 and OCE #2129697

A dinoflagellate-infecting giant virus with a micron-length tail | bioRxiv https://www.biorxiv.org/content/10.1101/2025.07.19.665647v1?rss=1

Preprint: “Structural modeling reveals viral proteins that manipulate host immune signaling”

Using AI-guided structural modeling, we find new families of viral proteins that sequester or cleave host immune signaling molecules

Congrats Nitzan Tal!

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

SAM-AMP lyases in type III CRISPR defence Abstract. Type III CRISPR systems detect non-self RNA and activate the enzymatic Cas10 subunit, which generates nucleotide second messengers for activation

Here we show how the type III signalling molecule SAM-AMP is bound and degraded by a specialised lyase enzyme encoded in cellular and phage genomes. More great work by @haotianchi.bsky.social and the team. @uniofstandrews.bsky.social
academic.oup.com/nar/article/...

must-read for phageophiles 👇 from sigal ben-yehuda's lab

"𝗬𝗷𝗯𝗛 𝗮𝗻𝗱 𝘁𝗵𝗲 𝗱𝗶𝘃𝗶𝘀𝗶𝗼𝗻 𝗺𝗮𝗰𝗵𝗶𝗻𝗲𝗿𝘆 𝗷𝗼𝗶𝗻𝘁𝗹𝘆 𝗮𝗰𝘁 𝘁𝗼 𝗰𝗼𝗻𝗳𝗶𝗻𝗲 𝗽𝗵𝗮𝗴𝗲 𝗰𝗼𝗺𝗽𝗼𝗻𝗲𝗻𝘁𝘀" in Gram-positives (𝘉. 𝘴𝘶𝘣𝘵𝘪𝘭𝘪𝘴)

🙏 @bacteriophile.bsky.social for pointing this out

#PhageSky #MicroSky

We have an open engineer position to work on type IX secretion (T9SS), under the supervision of @doan_thierry (collab with HP Fierobe & A. Tolonen). 1-year contract, renewable up to 3.5 years. Please apply here or forward to anyone potentially interested:

emploi.cnrs.fr/Offres/CDD/U...

Gene expression and co-expression heterogeneity patterns and biodemography analyses during the cell cycle encourage aging studies in archaea - GeroScience One of the prokaryotic partners at the origin of eukaryotes was an archaeon, but do archaea age, and if so, how? Uncovering aging in Archaea might provide more general clues about cellular senescence ...

link.springer.com/article/10.1...

Archaeal cell have a hard start in life, dying in excess around cell division, and then, their risk of dying decreases.
Is it aging? Is it #ontogenescence?
Do archaeal cells age?
Can archaeal cells rejuvenate by asymetric cell division?
#archaea #aging #rejuvenation Thanks @mkrupovic.bsky.social

Congrats Simonetta dna Marc! Well deserved! 👏👏👏

Thanks! Looks good.

Excellent resource! Thank you. What was the fraction of PHROGs which could be confidently modeled?

We made structural predictions of representatives of each #PHROG from #phage genomes, and put the whole lot online. You can browse through montages or go to your favourite phrog directly and download its PDB.

💻🧬 #phagesky

linsalrob.github.io/PHROG_struct...

It's been a great few days hosting Eugene Koonin in St Andrews @uniofstandrews.bsky.social , where he was awarded an honorary degree in recognition of his stellar contributions to molecular biology and comparative genomics. Here with @tatianadimitriu.bsky.social

Characterizing organisms from three domains of life with universal primers from throughout the global ocean - Scientific Data Scientific Data - Characterizing organisms from three domains of life with universal primers from throughout the global ocean

Please Re-Post. Our global GRUMP microbial ocean database is out in Scientific Data! Unfractionated, single universal PCR, with Archaea, Bacteria, and Eukaryotes all on the same scale with the same denominator. Pole to pole, depths to 6000m. Lots of metadata. www.nature.com/articles/s41...

Electron flow in hydrogenotrophic methanogens under nickel limitation - Nature Two distantly related methanogens shift the methanogenic pathway under nickel limitation, suggesting that methanogens adapt to changing bioavailability of nickel by rerouting electron flow between two...

Our new study shows how nickel limitation changes electron flow in methanogens.
@nature.com
#methanogens #methane #archaea
www.nature.com/articles/s41...

Now online - the Review "Histone-mediated chromatin organization in prokaryotes and viruses" from @samuelschwab.bsky.social‬ @vikramalva.bsky.social @damelab.bsky.social‬ and co.

#histones #DNAorganization #chromatin #eukaryogenesis

Read it here 👉 authors.elsevier.com/sd/article/S...

Elated to have our pre-print now published in @natcomms.nature.com #ArchaeaSky #Microbiology #MEvoSky
rdcu.be/euila
Our main results stay the same: S. islandicus follows a cell cycle akin to that of some eukaryotes, like the budding yeast, with cellular processes cycling similarly.
old🧵cited below👇

Thank you, Thibaut!