Structural basis for DNA processing and membrane translocation by ComEC in natural transformation Natural transformation is one of the major pathways of horizontal gene transfer in bacteria, enabling the acquisition of extracellular DNA and its integration into the host genome. ComEC is a membrane...

ComEC structure is out!! 😍
Congratulations to the authors! That’s not an easy one. We have been trying for years to get that structure…
We failed and gave up.

Excited to share our new paper out today in @science.org 🎉

We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩

Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...

How diverse is bacterial immunity ?

We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...

Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

New preprint alert!!! 🚀🤓 We are very happy to finally share this with the world — the result of seven years of work and a new tool to study integrons and discover new functions encoded in these bacterial platforms.

If you want to know more, here is a thread 🧵
www.biorxiv.org/content/10.6...

Reversible DNA condensation drives natural transformation

@natcomms.nature.com from Keith Mickolajczyk, Matthew Neiditch, and David Dubnau

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

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.

Final version of our last paper is out!
www.nature.com/articles/s41...

🚨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...

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

➡️ 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? 🤔

🧵👇

We're still looking for the sensing mechanism (riboswitch, TCS?).
If anyone is aware of some example of Ca2+ (at submillimolar concentration) inducing gene expression, please let me know. Thanks.

Le CIRI recrute un Maître ou une Maîtresse de conférences en Microbiologie médicale
Plus d'informations : ciri.ens-lyon.fr/MCU-microbio...

📢 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

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!

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

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!

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

Indeed, in an in vitro-generated transformation D-loop, CoiA specifically cleaves the displaced strand at the edge of the D-loop

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

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

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

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

#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
🧵⬇️

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!

My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵

🔁 🙏

#microSky #phagesky #UTIsky
@cnrs.fr

Une opportunité unique de former des étudiants talentueux à la biologie des bactéries à l'ENS Lyon et mener des recherches sur les phages, l'immunité bactérienne, le transfert génétique horizontal (HGT) et/ou les éléments génétiques mobiles au sein du département de bactériologie du CIRI.

Wonderful work! So satisfying to finally get a view of this critical step of natural transformation. Thank you for that.
Congratulations to all!

A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes | PNAS Natural genetic transformation is a conserved mechanism of bacterial horizontal gene transfer, which is directed entirely by the recipient cell and...

Pleased to share our recent article in PNAS - a collaboration with @jessicaandreani.bsky.social & Pablo Radicella, with important roles played by many members of each team.

A tripartite protein complex promotes DNA transport during natural transformation in Firmicutes www.pnas.org/doi/10.1073/...

MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Liverpool on Fin... PhD Project - MRC DiMeN Doctoral Training Partnership: Resistant zombies: how drug-resistance plasmids manipulate the behaviour of the opportunistic pathogen Pseudomonas aeruginosa at University of Li...

🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️

Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...

Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons Abstract. Integrons act as biobanks of gene cassettes conferring functions crucial for bacterial defense, including protection against phages and antibioti

Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5