Marie-Eve VAL

Exciting opportunity @pasteur.fr for junior scientists aiming to create their research group !

The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae Author summary This study charts the first genome-wide map of transfer RNA (tRNA) modifications in the cholera pathogen, Vibrio cholerae, revealing how chemical marks on tRNAs shape translation and st...

Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫
We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠
Huge thanks to amazing co-authors and collaborators!
@plos.org #rnasky #microsky #tRNAmodifications

With this working, as a first test we took two plasmids, identical save for 8 point mutations changing the color, and competed them against one another. Here’s a video of what it looked like when we activated the recombinase. You can see the two compete in real time: 4/

Cool work from Heath Murray's lab where they use Cas9 nickase to study how ssDNA breaks are repaired in Bacillus subtilis #MicroSky www.nature.com/articles/s41...

An Innovative Method for Measuring DNA Polymerase Fidelity In collaboration with New England Biolabs, the DNA Replication research group led by Ludovic Sauguet at the Institut Pasteur has published in Nucleic Acids Research an innovative approach based on Pac...

🧬 New method to map DNA polymerase errors with unprecedented precision.

Institut Pasteur researchers (Ludovic Sauguet's lab) developed a high-throughput approach using PacBio sequencing to characterize how DNA polymerases make mistakes.

In collaboration with @nebiolabs.bsky.social

Genome integrity relies on rapid recycling of DNA Pol III in bacteria | PNAS DNA replication requires precise coordination between DNA unwinding and DNA synthesis. In all domains of life, protein–protein interactions at the ...

Happy to share our most recent work www.pnas.org/doi/10.1073/.... Here we describe how efficient DNA replication in E. coli is dependent on an interaction between SSB-ssDNA and the DNA polymerase (Pol III). Thanks to all the co-authors for their hard work!

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf

High-throughput conjugation reveals strain specific recombination patterns enabling precise trait mapping in Escherichia coli Author summary Escherichia coli demonstrates a remarkable ability to adapt to diverse environments. This adaptability is in part connected to its ability to recombine incoming DNA in its chromosome, a...

#microsky 😮

journals.plos.org/plosgenetics...

Did you know most 'complete' Streptomyces genomes are missing their telomeres?

Thanks to David and Tues hard work, we now have a new tool to recover them!

A pleasure to be part of a team. :)

🦠🧪💻 #microsky

Thrilled to share our multidisiplinary work on how genome-wide DNA bridging by H-NS reshapes the stationary phase bacterial nucleoid and affects the transcriptional landscape. With Xindan Wang and @meyerroc.bsky.social
www.biorxiv.org/content/10.1...

Chromosome segregation dynamics during the cell cycle of Staphylococcus aureus - Nature Communications Our understanding of chromosome organization and dynamics in spherical bacteria, such as Staphylococcus aureus, remains limited. Here, the authors show that chromosome replication and cell division cycles are not synchronized in S. aureus, with cells exhibiting two segregated origins of replication at the start of the cell cycle.

Chromosome replication and cell division cycles are not synchronized in Staphylococcus aureus, with cells exhibiting two segregated origins of replication at the start of the cell cycle

#bacteria #microbiology

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

How do SMC complexes load onto DNA to get ready for loop extrusion?

@roisnehamelinf.bsky.social & co discovered that Wadjet, an SMC complex involved in bacterial DNA immunity, performs some impressive molecular gymnastics 🤸‍♂️🤸‍♂️🤸‍♂️.

Check out the new paper: www.cell.com/molecular-ce...

Finally out, such an awesome piece of work, very proud of this one: www.cell.com/cell-systems... #MicroSky

Uridine as a potentiator of aminoglycosides through activation of carbohydrate transporters Uridine boosts aminoglycoside treatment efficiency against antibiotic-susceptible as well as antibiotic-resistant E. coli strains.

So excited our antibiotic potentiation story is out 🤩 Led by the extraordinary @manonlang.bsky.social with @fox-science.bsky.social & @amazeld.bsky.social +amazing collaborators @immunobladder.bsky.social @imaneelmeouche.bsky.social 🦠 We believe it can make a difference in #AMR infections!

Efficient detection and typing of phage-plasmids Phage-plasmids are temperate phages that replicate as plasmids during lysogeny. Despite their high diversity, they carry genes similar to phages and plasmids. This leads to gene exchanges, and to the ...

🚨 New preprint! 🧬

𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect.

We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps:
✅ Accurate
✅ Sensitive
✅ Easy to use

📖 www.biorxiv.org/content/10.1...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

At last ! A tool specifically for phage-plasmid hunters. Check tyPPing by @karinailchenko.bsky.social and @eugenpfeifer.bsky.social

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes. Background: Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is w...

New preprint from the group: @lucydillon.bsky.social analysis of 16,000+ genomes finds Bacteria cannot combine certain resistance genes as they are mutually exclusive, forcing them down incompatible evolutionary paths.
biorxiv.org/content/10.1101/2025.08.20.671315v1
@jomcinerney.bsky.social

The interplay of membrane tension and FtsZ filament condensation on the initiation and progression of cell division in B. subtilis The first step of cell division is deforming the planar cell membrane inward towards the cytoplasm. As deforming membranes is energetically costly, biology has developed various protein systems to acc...

I’m excited that the work by Diego Ramirez and Lei Yin is out, where they gained several key insights into what provides the force underlying bacterial cell division doi.org/10.1101/2025....

To divide, cells must first bend the membrane inward, a process that’s energetically expensive

Genetic determinants of pOXA-48 plasmid maintenance and propagation in Escherichia coli - Nature Communications pOXA-48 plasmids have emerged as key vectors of carbapenem resistance within Enterobacteriaceae. In this study, the authors use a transposon sequencing (Tn-seq) approach to identify genetic determinan...

Our paper “Genetic determinants of pOXA-48 plasmid maintenance and propagation in Escherichia coli” is now online in @natcomms.nature.com ✨
👉 www.nature.com/articles/s41...
@cnrs-rhoneauvergne.bsky.social @mmsb-lyon.bsky.social

Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens Nature Communications - This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the...

This work is finally published! 🥳🧬
Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14

#microsky In this review, we summarize the current literature across bacterial phyla on large extrachromosomal replicons. Current Opinion in Microbiology: doi.org/10.1016/j.mi....

Congratulations to PhD students Jasmin Ostermayer and Noa Guzzi (co–first authors 🎉), together with Jakub Czarnecki and Alfonso Soler-Bistué, for compressing the diverse, lineage-wide literature on large extrachromosomal replicons into <5000 words and 80 references 😅

Taming wild replicons: evolution and domestication of large extrachromosomal replicons Bacterial genomes often contain extrachromosomal replicons (ERs), ranging from small, mobile plasmids to large, stably inherited elements, such as meg…

For those who love bacterial replicons, The ultimate review, from our lab, signed by the master of their evolution.
‪@val-meve.bsky.social‬ www.sciencedirect.com/science/arti...

Deep learning reveals antibiotics in the archaeal proteome - Nature Microbiology Use of artificial intelligence to mine proteomes of archaea led to the discovery of archaeasins, antimicrobials that kill drug-resistant bacteria in laboratory and animal models, offering a promising source of future antibiotics.

A paper in Nature Microbiology reports that the use of AI to mine proteomes of archaea led to the discovery of archaeasins, antimicrobials that kill drug-resistant bacteria in laboratory and animal models, offering a promising source of future antibiotics. #medsky 🧪

An orthogonal T7 replisome for continuous hypermutation and accelerated evolution in E. coli Systems that perform continuous hypermutation of designated genes without compromising the integrity of the host genome can substantially accelerate the evolution of new or enhanced protein functions....

#NatMicroPicks

Synthetic evolution overdrive 🦠🔧🚅

A highly mutagenic DNA replication system speeds up evolution in Escherichia coli, without harming the host, opening a new way to accelerate protein engineering.

#SynBio #MicroSky

www.science.org/doi/10.1126/...

A two year post-doctoral position at the BacterialGenome Plasticity Unit starting October 1st - Research

A 2-year postdoc position in my lab, under the supervision of P-Alex Kaminski, on Z-DNA phages and the benefit given by ZTGC DNA and the replication machinery, with attempt to create a Z based minireplicon
research.pasteur.fr/en/job/a-two...

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/...

AlphaFold - A practical guide AlphaFold - A practical guide

Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!

There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...