Xavier Charpentier

Xavier Charpentier

@labxc.bsky.social

Group leader. HGT in bacterial pathogens. Acinetobacter, Legionella. Natural transformation. AMR. MGEs. Centre International de Recherche en Infectiologie

724 followers408 following48 posts

Xavier Charpentier reposted

New preprint from my Post-Doc in the Swarts lab How are the guide RNAs generated that direct prokaryotic Argonautes to invading DNA? This has been an open question for >10 years. Our new study reveals that the host housekeeping enzyme RNase E is responsible! A 🧵: 1/14

#microsky Massive update of preprint with @polardlab.bsky.social! Bacteria have evolved two systems to recombine extracellular DNA www.biorxiv.org/content/10.1... Kudos to lead authors Léo Hardy, Violette Morales and Clothilde Rousseau, and to outstanding Dalia's lab and @epcrocha.bsky.social 🧵⬇️

biorxiv.orgTwo D-loop resolution systems enable natural genetic transformation in bacteriaNatural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds by the capture and internalization of exogenous DNA in linear single strands, ultimately integrated in the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has co-evolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-20-CE12-0004, ANR-10-BLAN-1331, ANR-17-CE13-0031, ANR-22-CE44-0044, ANR-10-LABX-62-IBEID, PIA/ANR-16-CONV-0005 Fondation pour la Recherche Médicale, https://ror.org/04w6kn183, FDT202001010890 European Union's Horizon research and innovation programme. Marie Skłodowska-Curie Postdoctoral Fellowships, 101208987 National Institute of Health, USA, R35GM128674

Xavier Charpentier reposted

Authors!🚨 While you scramble for scarce $ 🤔 “Springer Nature reports revenue growth of 6.2%..and adjusted operating profit growth of 7.7%. They reported even more stunning submission growth of 30% and published article growth of 13%.” Publishing in society journals helps YOU not them👇🏻. Pass it on.

Xavier Charpentier reposted

Xavier Charpentier reposted

Xavier Charpentier reposted

Xavier Charpentier reposted

There are a few parts of this preprint that don't add up in my opinion. 1. They find 10% of papers change their primary conclusions from preprint to publication. But if the primary conclusion of a paper is rebutted in peer review, isn't it a common+appropriate outcome for it to not be published?

Richard Sever@richardsever.bsky.social

“move from preprint to peer-reviewed publication leaves the central claims of most abstracts intact, indicating preprints are a reliable source…papers that were never posted as preprints were retracted at roughly twice the rate of those that were…” www.biorxiv.org/content/10.6...

Xavier Charpentier reposted

We are looking for a motivated PhD student in phage genomics! Please find the details attached. Application deadline 24/07. Don't hesitate to spread the word!

Xavier Charpentier reposted

Our paper out in Science today: The Metis defense system senses molecular byproducts released when a phage degrades the bacterial genome, and then prevents replication of the phage in the infected cell Congratulations @ostermanilya.bsky.social and co-authors!

science.orgBacteria sense virus-induced genome degradation via methylated mononucleotidesPhages often degrade the genome of their bacterial host to individual nucleotides. Here we describe Metis, a bacterial defense system that directly senses phage-mediated host genome degradation. Metis...
Osterman Ilya@ostermanilya.bsky.social

Excited to share that our Metis story is now published in Science! 🎉 Bacteria can sense phage-induced degradation of their genome and activate immunity. Many thanks to everyone who contributed to this work. 📄 www.science.org/doi/10.1126/... More details in my earlier thread 🧵⬇️

In all, we unambiguously demonstrate that bacteria have evolved immune systems to specifically defend against conjugative plasmids. Multiple systems remain to be discovered, with fundamental implications on antimicrobial resistance and plasmid ecology and evolution.

Triggering cell death upon conjugation is unexpected. This extreme response confers population-level plasmid protection like defense systems do against virulent phages. Plasmid spread is likely a greater threat to bacterial populations than currently believed.

We could see this happening under the microscope in the TacC lab. Cells expressing Namtar stop growing as soon as they receive the plasmid, that is visualized as bright green ParB-mChartreuse foci.

The two other genes encode the new Namtar and Attar immune systems, also widespread in bacteria. They are membrane-associated proteins defending against R388. Namtar depends on sensing VirB8, while Attar senses VirB2. Both trigger a non-growing, ATP-depleted state. Let's call this death.

Which genes/function could limit conjugation? Tn mutagenesis revealed the culprits in 12 strains. Capsule is one of the barriers. Interestingly, H-NS expression can sometimes lift the barriers. Most importantly 4 genes of patchy distribution specifically block R388 or RP4 conjugation.

Two of them are part of the same family encoding the new Ishtar immune system that is widespread in Bacteria, and also found in Archaea. Ishtar carries a HEPN domain and specifically promotes loss of RP4 plasmid.

Is conjugation really so efficient? Are there barriers? Do bacteria defend against it? Ludovic tested 364 A. baumannii strains as recipients of the R388 and RP4 plasmids. This revealed that resistance to conjugation is the norm and is a fast-evolving phenotype.

Xavier Charpentier reposted

🚨New paper alert 🚨 Here we tried to leverage an (incredible) metagenome time-series to better understand MGE diversity and activity in soil across decade(s). @scbagby.bsky.social has an amazing thread about this work with all the details - bsky.app/profile/scba...

nature.comMobile genetic elements shape microbial diversity and functions in thawing permafrost soils - Nature MicrobiologyAn 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.
Sarah Bagby@scbagby.bsky.social

Out today in Nature Microbiology: a paper that started in 2021 with an email from @sullivan-lab.bsky.social. Subject line: "Crazy ideas". www.nature.com/articles/s41... 1/23

Xavier Charpentier reposted

Extension of the deadline for latecomers. Register to the Secretion Days in Marseille !

Julien GIRAUD@juliengiraud.bsky.social

👉Reminder : FIVE DAYS LEFT👈 📅 Secretion Days 2026 will take place on October 8-9 in Marseille 🌊 🎤Invited speaker : Wilbert Bitter; @wilbertbitter.bsky.social 🆓 Free, spot are limited ! 📥 Registration is open until June 15 via the following link: docs.google.com/forms/d/e/1F...

Xavier Charpentier reposted

Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.

bioRxiv Synthetic Biology@biorxiv-synthbio.bsky.social

Bridge recombinase enables versatile rewriting of bacterial genomes https://www.biorxiv.org/content/10.64898/2026.04.29.721476v1

Xavier Charpentier reposted

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

Xavier Charpentier reposted

Xavier Charpentier reposted

🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process. www.biorxiv.org/content/10.6...

Xavier Charpentier reposted

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

Jorge Moura de Sousa@jmouradesousa.bsky.social

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

Xavier Charpentier reposted

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔 🧵👇

biorxiv.orgbiorxiv.org

Xavier Charpentier reposted

📢 Recrutement d’un(e) Maître(sses) de conférence en Biochimie générale, spécialité bactériologie moléculaire à MMSB 🔬Recherche *Immunité anti-phages *Réponse au stress, modulation de la croissance bactérienne ✉️ christophe.grangeasse@cnrs.fr 📚Enseignement : Université Lyon I ✉️ patrice.gouet@ibcp.fr

#microsky Massive update of preprint with @polardlab.bsky.social! Bacteria have evolved two systems to recombine extracellular DNA www.biorxiv.org/content/10.1... Kudos to lead authors Léo Hardy, Violette Morales and Clothilde Rousseau, and to outstanding Dalia's lab and @epcrocha.bsky.social 🧵⬇️

biorxiv.orgTwo D-loop resolution systems enable natural genetic transformation in bacteriaNatural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds by the capture and internalization of exogenous DNA in linear single strands, ultimately integrated in the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has co-evolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-20-CE12-0004, ANR-10-BLAN-1331, ANR-17-CE13-0031, ANR-22-CE44-0044, ANR-10-LABX-62-IBEID, PIA/ANR-16-CONV-0005 Fondation pour la Recherche Médicale, https://ror.org/04w6kn183, FDT202001010890 European Union's Horizon research and innovation programme. Marie Skłodowska-Curie Postdoctoral Fellowships, 101208987 National Institute of Health, USA, R35GM128674
View full thread

Without the nuclease/helicase, the rare recombination events are very short. Hence, bacteria have evolved two distinct systems to efficiently resolve the D-loop and generate large recombination events by transformation

While YraN is likely guided by ComM to target the D-loop, CoiA which has replaced YraN in Bacillota, has evolved to specifically recognize the 3-strand junction. Most bacteria carry one of these systems, one more evidence that natural transformation is a common feature in bacteria!

#microsky Massive update of preprint with @polardlab.bsky.social! Bacteria have evolved two systems to recombine extracellular DNA www.biorxiv.org/content/10.1... Kudos to lead authors Léo Hardy, Violette Morales and Clothilde Rousseau, and to outstanding Dalia's lab and @epcrocha.bsky.social 🧵⬇️

biorxiv.orgTwo D-loop resolution systems enable natural genetic transformation in bacteriaNatural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds by the capture and internalization of exogenous DNA in linear single strands, ultimately integrated in the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has co-evolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-20-CE12-0004, ANR-10-BLAN-1331, ANR-17-CE13-0031, ANR-22-CE44-0044, ANR-10-LABX-62-IBEID, PIA/ANR-16-CONV-0005 Fondation pour la Recherche Médicale, https://ror.org/04w6kn183, FDT202001010890 European Union's Horizon research and innovation programme. Marie Skłodowska-Curie Postdoctoral Fellowships, 101208987 National Institute of Health, USA, R35GM128674
View full thread

Cleaving the displaced strand might be critical to allow for the helicase-driven extension of the D-loop. In vivo, genetic assays show that CoiA assists D-loop extension by the DnaB-type RadA helicase. Similarly, YraN assists, and interacts with, the transformation-specific MCM-type ComM helicase

We analyzed hundreds of recombinaison events to understand how the two nuclease/helicase systems (YraN/ComM and CoiA/RadA) enable efficient transformation. The defects in recombination in the absence of these very different nuclease/helicase systems are strinkingly similar!

#microsky Massive update of preprint with @polardlab.bsky.social! Bacteria have evolved two systems to recombine extracellular DNA www.biorxiv.org/content/10.1... Kudos to lead authors Léo Hardy, Violette Morales and Clothilde Rousseau, and to outstanding Dalia's lab and @epcrocha.bsky.social 🧵⬇️

biorxiv.orgTwo D-loop resolution systems enable natural genetic transformation in bacteriaNatural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds by the capture and internalization of exogenous DNA in linear single strands, ultimately integrated in the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has co-evolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-20-CE12-0004, ANR-10-BLAN-1331, ANR-17-CE13-0031, ANR-22-CE44-0044, ANR-10-LABX-62-IBEID, PIA/ANR-16-CONV-0005 Fondation pour la Recherche Médicale, https://ror.org/04w6kn183, FDT202001010890 European Union's Horizon research and innovation programme. Marie Skłodowska-Curie Postdoctoral Fellowships, 101208987 National Institute of Health, USA, R35GM128674
View full thread

Could the nucleases be helping resolve the D-loop? Biochemical analyses show that YraN is an endonuclease, cleaving ssDNA. CoiA is more specific, cleaving ssDNA if it's branching out of dsDNA. Both proteins might cleaved the parental ssDNA displaced by the transforming DNA molecule

#microsky Massive update of preprint with @polardlab.bsky.social! Bacteria have evolved two systems to recombine extracellular DNA www.biorxiv.org/content/10.1... Kudos to lead authors Léo Hardy, Violette Morales and Clothilde Rousseau, and to outstanding Dalia's lab and @epcrocha.bsky.social 🧵⬇️

biorxiv.orgTwo D-loop resolution systems enable natural genetic transformation in bacteriaNatural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds by the capture and internalization of exogenous DNA in linear single strands, ultimately integrated in the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has co-evolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-20-CE12-0004, ANR-10-BLAN-1331, ANR-17-CE13-0031, ANR-22-CE44-0044, ANR-10-LABX-62-IBEID, PIA/ANR-16-CONV-0005 Fondation pour la Recherche Médicale, https://ror.org/04w6kn183, FDT202001010890 European Union's Horizon research and innovation programme. Marie Skłodowska-Curie Postdoctoral Fellowships, 101208987 National Institute of Health, USA, R35GM128674
View full thread

As they actively import DNA, bacteria process it into ssDNA. Then, RecA-dependent homology search leads the ssDNA to invade the chromosomal DNA, generating a 3-strand intermediate called a D-loop. How this structure is resolved to stably integrate the transforming DNA is unknown

Our two labs separetely found that transformation requires a nuclease. CoiA in Streptococcus pneumoniae and a protein of unknown function in Legionella/Acinetobacter, YraN. CoiA and YraN are different proteins of the PD-(D/E)XK family of phosphodiesterases. Most bacteria possess one or the other

#microsky Massive update of preprint with @polardlab.bsky.social! Bacteria have evolved two systems to recombine extracellular DNA www.biorxiv.org/content/10.1... Kudos to lead authors Léo Hardy, Violette Morales and Clothilde Rousseau, and to outstanding Dalia's lab and @epcrocha.bsky.social 🧵⬇️

biorxiv.orgTwo D-loop resolution systems enable natural genetic transformation in bacteriaNatural transformation is a widespread mechanism driving genetic exchanges in bacteria. It proceeds by the capture and internalization of exogenous DNA in linear single strands, ultimately integrated in the genome by homologous recombination. It is unknown how the RecA-directed D-loop intermediate of this dedicated recombination pathway is processed. We report that resolution of the transformation D-loop depends on two endonucleases of opposing phylogenetic distribution in bacteria. One is YraN, which has co-evolved and interacts with the ComM helicase, known to extend DNA recombination at the transformation D-loop. The other is CoiA, which is restricted to the Bacillota. CoiA is shown to be a resolvase of the transformation D-loop, extended by the RadA helicase in these species. We demonstrate that both YraN and CoiA act synergistically with their cognate helicases. These findings reveal that bacteria have evolved two helicase/nuclease pairs for the maturation and recombination extension of the transformation D-loop. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-20-CE12-0004, ANR-10-BLAN-1331, ANR-17-CE13-0031, ANR-22-CE44-0044, ANR-10-LABX-62-IBEID, PIA/ANR-16-CONV-0005 Fondation pour la Recherche Médicale, https://ror.org/04w6kn183, FDT202001010890 European Union's Horizon research and innovation programme. Marie Skłodowska-Curie Postdoctoral Fellowships, 101208987 National Institute of Health, USA, R35GM128674

Since the discovery of natural transformation by Frederick Griffith in 1928, an ever increasing number of bacteria have been found to be able to integrate extracellular DNA it in their genome. This allows for acquisition/loss of genes and polymophisms, with consequence on #AMR