Mart Krupovìč | Lightnews

Mart Krupovic

@mkrupovic.bsky.social

2.5K followers 450 following 87 posts

Virus origins/diversity/evolution; mobilome; Archaea.
Head of the Cell Biology and Virology of Archaea Unit at Institut Pasteur:
https://research.pasteur.fr/en/team/archaeal-virology/

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Biology 41%

Environmental science 29%

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Reposted by Mart Krupovìč

Jean-Yves Tinevez @jytinevez.bsky.social · 20h

New preprint alert!

We developed an automated framework to optimize tracking pipelines for bacteria, along with a nice integration of tools for bacteria imaging, in the recently released TrackMate 8 (Fiji plugin).
www.biorxiv.org/content/10.6...

👇🧵

www.biorxiv.org

Reposted by Mart Krupovìč

Oleksandr Maistrenko @omaistrenko.bsky.social · 21h

I invite you to check our paper entitled “Rebuilding Ukraine’s capacity for fundamental research in evolutionary biology” doi.org/10.1038/s415... in @natecoevo.nature.com about the Ukrainian School in Evolutionary Biology #USEB we organized in 2025.
#biology #evolution #school #science #Ukraine

Mart Krupovic @mkrupovic.bsky.social · 22h

Congrats Rodrigo!

Reposted by Mart Krupovìč

Yann Moalic @drym.bsky.social · 4d

Archaeal G-quadruplexes: a novel model for understanding unusual DNA/RNA structures across the tree of life url: academic.oup.com/nar/article/...

Archaeal G-quadruplexes: a novel model for understanding unusual DNA/RNA structures across the tree of life

Abstract. Archaea, a domain of microorganisms found in diverse environments, including the human microbiome, represent the closest known prokaryotic relati

academic.oup.com

Reposted by Mart Krupovìč

Vardilab @vardilab.bsky.social · 4d

🌊Paper announcement! 📣
Viral infections rewire the metabolic makeup of their host and thereby create distinct chemical signatures. Can we use metabolic biomarkers to diagnose infections of algal blooms in the ocean?
Well, take a look at our new article led by Conny Kuhlisch in @pnas.org
>>

Mapping of the viral shunt across widespread coccolithophore blooms using metabolic biomarkers | PNAS

The viral shunt is a fundamental ecosystem process which diverts the flux of organic carbon fixed through photosynthesis during algal bloom events ...

doi.org

Reposted by Mart Krupovìč, Brett J. Baker

Pierre Simon Garcia @pierresimongarcia.bsky.social · 7d

Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).

Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution

HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...

www.nature.com

Reposted by Mart Krupovìč

Stèf Blanc @steffffff.bsky.social · 11d

BEWARE Last day for early bird
Join us to have science fun !!!!!!!
👇🏽
isdv2026.com

Beautiful Science Program 👍

If you miss it....you regret it !

15-19 June, 2026 | Ilhéus, Bahia, Brazil

Reposted by Mart Krupovìč

Laura Cantini @cantinilab.bsky.social · 11d

PhD position in my team at @pasteur.fr ! The selected canddiate will work on the development of new methods combining biophysicial and machine learning modelling for single-cell multi-omics spatiotemporal data.

emploi.cnrs.fr/Offres/Docto...

Portail Emploi CNRS - Offre d'emploi - PhD (M/F) in development of machine learning methods for single-cell omics data integration

Assurez-vous que votre profil candidat soit correctement renseigné avant de postuler

emploi.cnrs.fr

Reposted by Mart Krupovìč

Sorek Lab @soreklab.bsky.social · 11d

We found a new mode by which bacteria deplete NAD+ to protect from phages. And then we found how phages overcome this defense

Discovered by talented biochemist Dr Ilya Osterman, read the preprint: tinyurl.com/Narp-ap

A thread 🧵

Bacterial defense via RES-mediated NAD+ depletion is countered by phage phosphatases

Many bacterial defense systems restrict phage infection by breaking the molecule NAD+ to its constituents, adenosine diphosphate ribose (ADPR) and nicotinamide (Nam). To counter NAD+ depletion-mediated defense, phages evolved NAD+ reconstitution pathway 1 (NARP1), which uses ADPR and Nam to rebuild NAD+. Here we report a bacterial defense system called aRES, involving RES-domain proteins that degrade NAD+ into Nam and ADPR-1″-phosphate (ADPR-1P). This molecule cannot serve as a substrate for NARP1, so that NAD+ depletion by aRES defends against phages even if they encode NARP1. We further discover that some phages evolved an extended NARP1 pathway capable of overcoming aRES defense. In these phages, the NARP1 operon also includes a specialized phosphatase, which dephosphorylates ADPR-1P to form ADPR, a substrate from which NARP1 then reconstitutes NAD+. Other phages encode inhibitors that directly bind aRES proteins and physically block their active sites. Our study describes new layers in the NAD+-centric arms race between bacteria and phages and highlights the centrality of the NAD+ pool in cellular battles between viruses and their hosts. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, ERC-AdG GA 101018520 Israel Science Foundation, MAPATS grant 2720/22 Deutsche Forschungsgemeinschaft, SPP 2330, grant 464312965 Minerva Foundation with funding from the Federal German Ministry for Education and Research research grant from Magnus Konow in honor of his mother Olga Konow Rappaport Ministry of Aliyah and Immigrant Absorption, https://ror.org/05aycsg86 Clore Scholars Program

tinyurl.com

Reposted by Mart Krupovìč

BejaLab @bejalab.bsky.social · 19d

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41...

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology

Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...

www.nature.com

Reposted by Mart Krupovìč

Rubén González @rubengonzalez.bsky.social · 19d

Not all bacteria are beneficial in every context.

We found that enriching Drosophila with a commensal bacterium reduces tolerance to viral infection. The effect was virus-specific and occurred without changes in viral load, immune gene expression or intestinal damage.

rdcu.be/eZ4Sd

Microbiome composition modulates the lethal outcome of Drosophila A virus infection

rdcu.be

Reposted by Jesse M. Shapiro, Simon Roux, Mart Krupovìč

A. Murat Eren (Meren) @merenbey.bsky.social · 21d

We just released #anvio v9, "eunice" 🎉

This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.

Read the release notes:

github.com/merenlab/anv...

Visit our up-to-date web page:

anvio.org

Reposted by Mart Krupovìč

Milot Mirdita @milot.bsky.social · 21d

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning

Mirdita Lab builds scalable bioinformatics methods.

mirdita.org

Reposted by Mart Krupovìč

Victor Tobiasson @victortobiasson.bsky.social · 22d

Dominant contribution of Asgard archaea to eukaryogenesis.

tldr; Best guess, ~ 50% of conserved eukaryotic protein families are from from Asgard archaea!

#science #biology #evolution #nature #bioinformatics

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

Dominant contribution of Asgard archaea to eukaryogenesis - Nature

A survey of the reconstructed gene set of the last eukaryotic common ancestor shows a consistent link between Asgard archaea and the origin of numerous, functionally diverse eukaryotic genes, dem...

www.nature.com

Reposted by Simon Roux, Mart Krupovìč

Franklin Nobrega @fnobrega.bsky.social · 23d

Preprint out: We characterise PUA-Cal-HAD, a widespread bacterial antiphage defence family. An infection cue switches a preassembled complex into an immune filament that drains dNTPs via a coupled two-enzyme cascade, and phage DNA mimics can block filament assembly (anti-polymerisation).

A methylome-derived m6-dAMP trigger assembles a PUA-Cal-HAD immune filament that depletes dNTPs to abort phage infection

Bacteria must distinguish phage attack from normal homeostatic processes, yet the danger signals that trigger many defence systems remain unknown. Here, we show that a PUA-Calcineurin-CE-HAD module from Escherichia coli ECOR28 confers broad anti-phage protection by binding Dam-methylated deoxyadenosine monophosphate (m6-dAMP) generated during phage-induced chromosome degradation. Ligand binding converts a preassembled PUA-Calcineurin-CE hexamer loaded with six HAD phosphatases into a polymerising filament. The filament acts as a high-flux dNTP sink through a two-enzyme cascade: HAD first dephosphorylates dATP to dADP, and Calcineurin-CE then converts dADP to dAMP. dNTP collapse halts phage replication and enforces abortive infection. Multiple mobile-element DNA mimic proteins block filament assembly, revealing a direct phage counter-defence. More broadly, our findings extend a conserved, cross-kingdom paradigm of immune filament assembly to nucleotide-depletion antiviral defence and suggest modified-nucleotide sensing by related PUA-Calcineurin-CE modules as a widespread, underappreciated bacterial strategy. ### Competing Interest Statement The authors have declared no competing interest. NIHR Southampton Biomedical Research Centre, https://ror.org/01qqpzg67, Postdoctoral Bridging Fellowship F.L.N. is supported by a Wessex Health Partners (WHP) and National Institute for Health and Care Research Wessex Experimental Medicine Network (NIHR WEMN), Seed fund National Institutes of Health, GM145888, U24 GM129539) Maloris Foundation Memorial Sloan Kettering Cancer Center, P30-CA008748 Simons Foundation, SF349247 New York State Assembly

www.biorxiv.org

Reposted by Mart Krupovìč

Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 24d

𝘐𝘮𝘢𝘨𝘪𝘯: an integrase-like gene conserved across malacostracan crustaceans derived from a Ginger1 DNA transposon
We discovered a domesticated transposon in crustaceans, which has abandoned its mobility for a host function (likely reproductive).
doi.org/10.1093/gbe/...

Figure 1. Imagin, a multi-exon integrase-like gene in malacostracan crustaceans.
(A) Structure of the PjImagin gene. The transcript is shown in light blue and the CDS in white. The YPYY motif is colored yellow, the H2C2 zinc finger is colored sky blue, the defunct DDE catalytic core is colored in pink, and the disordered region is shaded in gray. Gray vertical lines denote the positions of key residues denoted in panels C and D, with
the last two lines being shaded to indicate the corresponding positions for the lost D and E residues (Panel E).
(B) The genomic context of PjImagin and orthologs. PjImagin is flanked by exons 14 and 15 of methylmalonyl-CoA mutase, mitochondrial-like (MMUT) gene, which runs on the opposite strand. Note that the Imagin gene of the swimming crab (Portunus trituberculatus) lies on an unrelated position. MMUT CDS is colored green, and MMUT exons corresponding to exons 14 and 15 of P. japonicus MMUT are connected with light green ribbons. CDS of other genes are shaded gray.
(C) Domain architectures of malacostracan Imagin proteins. The coloring scheme follows that of panel (A).
(D) Conservation of the YPYY motif and the H2C2 (HHCC) zinc-finger domain in integrase proteins. Species names are listed on the left, with protein accession numbers provided on the right. Entries Ginger1-1_HM, Ginger1-2_HM, and Ginger1-3_HM were adopted from (Bao et al. 2010).
(E) Loss of the DDE catalytic residues in crustacean Imagin proteins. Species names are listed on the left, with protein accession numbers provided on the right. Note that some residues may be missing from this alignment because regions containing long gaps were automatically suppressed by DALI. Each residue is shaded by background color according to the secondary structure assignments by DSSP: light green: loop; dark green: helix; blue: strand. Conserved aspartic acid (D) and glutamic acid (E) residues comprising the DDE motif are highlighted in black.

Figure 3. Imagin is a domesticated Ginger1 DNA transposon.
(A) Maximum-likelihood phylogenetic tree of 121 DDE integrases and derivatives (136 sites; model: VT+R6).
(B) Subtree of (A) showing the phylogenetic relationships of Ginger1-like elements. The bar beside the tree indicates amino acid substitutions per site. The slashed values beside the nodes indicate the support values for the ultrafast bootstrap test followed by the SH-like approximate likelihood ratio test (1,000 trials each).

Figure 2. Phylogenetic analysis of decapod Imagin proteins.
A total of 463 sites were used for the maximum-likelihood phylogenetic analysis using IQTREE v3.0.1 (substitution model: Q.MAMMAL+F+I+G4). The slashed values beside the nodes indicate the support values for the ultrafast bootstrap test followed by the SH-like approximate likelihood ratio test (1,000 trials each). The bar indicates amino acid substitutions per site. Euphausiacea and Stomatopoda were used as the outgroup. Imagin proteins from brachyuran crabs formed a long branch relative to the other taxa, suggesting accelerated evolution following the translocation event in this lineage.

Reposted by Mart Krupovìč

Karim Majzoub @karimaj.bsky.social · 24d

Zoe Denis a PhD student in our lab , describing the first marsupial deltavirus ! :)

A replication-competent deltavirus from the marsupial fat-tailed dunnart Sminthopsis crassicaudata

Deltaviruses are circular, negative-sense RNA agents that replicate autonomously but depend on heterologous envelope glycoproteins for spread. Only partial sequences of deltaviruses had been reported ...

www.microbiologyresearch.org

Mart Krupovic @mkrupovic.bsky.social · 24d

If you are interested in ssDNA viruses of bacteria, archaea or eukaryotes (yes, from all walks of life!), this is the conference for you - International Symposium on ssDNA Viruses (ISS3DV)! isdv2026.com
The deadline for the early bird registration is approaching...

Reposted by Mart Krupovìč

Nature Communications @natcomms.nature.com · 24d

#Virology

Herpesviruses exploit a cellular membrane protein, once thought to transport chloride, to escape the nucleus by tapping into an ancient membrane fusion process

ER protein CLCC1 promotes nuclear envelope fusion in herpesviral and host processes - Nature Communications

Herpesvirales utilize a unique nuclear egress route for capsid export. Here the authors show that herpesviruses exploit a cellular membrane protein, once thought to transport chloride, to facilitate membrane fusion and egress from the nucleus.

dlvr.it

Reposted by Mart Krupovìč

Stèf Blanc @steffffff.bsky.social · 25d

Deadline approaching
Do Not Forget to join us !!!
Beautiful Science program 👍🏻
👇🏼

isdv2026.com

Reposted by Håvard Kauserud, Mart Krupovìč

BejaLab @bejalab.bsky.social · 26d

Dominant contribution of Asgard archaea to eukaryogenesis www.nature.com/articles/s41...

Reposted by Mart Krupovìč

Manuel Ares-Arroyo @aresarroyom.bsky.social · 27d

Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.

Here we explore the conjugative capacity of these mysterious Genomic Islands.

www.biorxiv.org/content/10.6...

www.biorxiv.org

Reposted by Mart Krupovìč

George Bouras @gbouras13.bsky.social · 27d

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Reposted by Mart Krupovìč

Thelonevirologist @thelonevirologist.bsky.social · 28d

Metabolic hijackers: how viral proteins redefine host cell landscapes journals.asm.org/doi/10.1128/...

Metabolic hijackers: how viral proteins redefine host cell landscapes | Journal of Virology

Viruses have evolved numerous strategies to ensure successful infection and replication within hosts. One of these is the manipulation of host metabolism. As obligate intracellular parasites, viruses are dependent on their hosts for much of the biological machinery needed for replication. Since many viruses are also metabolically inert, they rely on hijacking host metabolic processes to create a more favorable intracellular environment, ensuring a consistent availability of resources required to produce viral progeny (1).

journals.asm.org

Reposted by Mart Krupovìč

Maya Voichek @mayavoichek.bsky.social · 29d

The (Yoav) Voichek lab has opened its gates at the Weizmann Institute, and is actively recruiting students and researchers at all levels - come explore gene regulation and computational genomics in a fun, friendly sprouting lab 🤗🥼⚗️🧪
www.weizmann.ac.il/plants/voichek

Reposted by Simon Roux, Mart Krupovìč

Ingrida Olendraite @ingrida.bsky.social · Jan 9

Save the date for phylogenetics!

RNA virus Journal Club returns ( @rdrpsummit.bsky.social ) with @evogytis.bsky.social intro to his "Baltic" - python module to visualise phylogenetic trees.

January 15th (Thu) - EEST Vilnius Time 3:00 PM

Join slack for updates: join.slack.com/t/rdrp-io/sh...

Reposted by Mart Krupovìč

Juha Huiskonen @juhahuiskonen.bsky.social · Jan 8

I am pleased to share our new paper in Molecular Cell:

“Capsid restructuring activates semi-conservative dsRNA transcription in cystovirus ɸ6.”

We visualized, in structural detail, how a double-stranded RNA virus switches from a quiescent to a transcriptionally active state.

Link in the comments

Reposted by Mart Krupovìč

Tominaga K. (tomiken) @pacyc184.bsky.social · Jan 6

A prophage-expressed type IV pilus component provides anti-phage defense: Cell Reports https://www.cell.com/cell-reports/fulltext/S2211-1247(25)01531-1?rss=yes

A prophage-expressed type IV pilus component provides anti-phage defense

Sztanko et al. demonstrate that Pseudomonas aeruginosa prophages encode proteins resembling the type IV pilus minor pilin protein, FimU. These prophage-expressed FimU proteins are incorporated into the pilus without disrupting pilus function and prevent the adsorption of phages that bind to the tip of the pilus, where FimU is located.

www.cell.com

Reposted by Mart Krupovìč

vinceconticello.bsky.social @vinceconticello.bsky.social · Jan 5

New manuscript alert. Turns out that calcium ion coordination may be a more common mechanism than we initially expected to trigger polymerization of extracellular filaments. @mikesleutel.bsky.social @vikramalva.bsky.social

www.biorxiv.org/content/10.6...