Mart Krupovic

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...

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...).

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 ...

🌊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
>>

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

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

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 🧵

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

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...

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...

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

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

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

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning Mirdita Lab builds scalable bioinformatics methods.

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

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...

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...

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).

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.

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/...

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 ...

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

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.

#Virology

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

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...

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

isdv2026.com

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

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/...

Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵

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).

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

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

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...

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

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.

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

New circoviruses discovered in pilot whales and orcas from the North Atlantic  A collaborative team of researchers has identified two previously unknown circoviruses in short-finned pilot whales and orcas from the Caribbean region of the North Atlantic Ocean.

Two previously unknown circoviruses have been identified in short-finned pilot whales and orcas from the North Atlantic, expanding the known diversity of circoviruses in marine vertebrates. doi.org/hbd8rg

Diverse bacterial pattern recognition receptors sense the conserved phage proteome Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...

NLR-like immunity in bacteria

A new study from the Alex Gao lab. The scope of this work is incredible!!!

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

From fibril to framework: P. abyssi AbpX illuminates a calcium-responsive family of microbial biomatrix proteins that form thermostable hydrogels Evolutionary pressure on microbial communities propagating under extreme environmental conditions often results in unique structural adaptations to promote cell survival. Here, we report an investigat...

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...

Endogenized polinton-like viruses in the dinoflagellate Oxyrrhis marina uncover novel PolB fusion Marine viruses are ubiquitous entities that impact the biology of a large fraction of prokaryotic and eukaryotic diversity. Dinoflagellates are heterotrophic, mixotrophic and photosynthetic eukaryotes...

Endogenized polinton-like viruses in the dinoflagellate Oxyrrhis marina uncover novel PolB fusion

www.microbiologyresearch.org/content/jour...

Are you a long-time fan of Archaea, an extremophile-phile, or are you simply curious?

Either way, we have good news.
We’re delighted to announce the 2026 EMBO Workshop on Archaea, 6–10 July.

Sign up: meetings.embo.org/event/26-arc...

We look forward to seeing you in Cambridge, UK.

Please repost!