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Florian Fournes

@flofournes.bsky.social
107 followers 137 following 5 posts

Bacterial Genomes Adaptation_ CBI-Université de Toulouse 🇨🇵

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Reposted by Florian Fournes
Jean-Yves Bouet @jyb-tlse.bsky.social · 10/08/2026
Happy to share our latest work: Fast assembly and in vivo coalescence of ParBf biocondensates involved in bacterial DNA partition academic.oup.com/nar/article/... Great thanks to all contributing authors and in particular Perrine Revoil and Linda Delimi for their fruitful collaborative interactions
academic.oup.com
Fast assembly and in vivo coalescence of ParBF biocondensates involved in bacterial DNA partition
Abstract. Faithful DNA segregation in bacteria relies on ParABS systems, in which ParB assembles into condensates at centromere-like parS sites, while the
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Reposted by Florian Fournes
Tominaga K. (tomiken) @pacyc184.bsky.social · 08/08/2026
Structural Maintenance of Chromosomes Complexes in Bacteria | Annual Reviews
annualreviews.org
Structural Maintenance of Chromosomes Complexes in Bacteria
Structural maintenance of chromosomes (SMC) complexes are conserved ATP-driven machines that organize, compact, and segregate genomes in all domains of life. Despite variation in subunit composition and regulation, all SMC complexes share a core structure and mechanism of action. Bacteria possess two major classes of SMC complexes, SMC-ScpAB and MukBEF, which function in chromosome compaction and segregation. In addition, some bacteria contain other SMC complexes or SMC-like systems such as MksBEF, Wadjet, RecN, and SbcC, each with specialized functions. Bacterial SMC complexes coordinate genome maintenance, DNA replication, DNA repair, plasmid defense, and cell physiology. In this review, we discuss the structure and function of these bacterial SMC complexes, highlighting the shared characteristics and unique strategies employed by each.
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Florian Fournes @flofournes.bsky.social · 02/07/2026
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Reposted by Florian Fournes
Lisanne Spenkelink @lisannes.bsky.social · 22/06/2026
The replication-risk sequence is an essential bacterial DNA sequence linked to DNA gap formation. For the first time, we directly observed this gap formation at single-molecule resolution! We show that the gaps occur exclusively on the lagging strand and reveal why. www.biorxiv.org/cgi/content/...
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Evgenii Protasov @evgenii-protasov.bsky.social · 07/06/2026
Mechanisms of chromosomal DNA replication in Escherichia coli and Bacillus subtilis #microbiology #chromosome #DNA #MicroSky @femsjournals.bsky.social @femsmicro.org doi.org/10.1093/fems...
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Justine Collier @justinecollier.bsky.social · 02/06/2026
I am delighted to share our latest preprint: doi.org/10.64898/202.... Fantastic work from my past and present lab members @flofournes.bsky.social, Sandra Martin and Nicolas Pellaton. Also many thanks to our precious collaborators @gruberlab.bsky.social and to @snsf.ch for funding this research.
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 30/05/2026
Genome replication and cell division control by the methylation-sensitive GcrA regulator in Agrobacterium tumefaciens www.biorxiv.org/content/10.64898/20…
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Marie-Eve VAL @val-meve.bsky.social · 04/05/2026
This one means a lot. Our paper, “Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome,” is out! doi.org/10.1038/s414...
doi.org
Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome - Nature Communications
Bacterial genomes often include extrachromosomal replicons, ranging from small plasmids to chromosome-scale replicons. Here, Czarnecki et al. analyse more than 40,000 complete bacterial genomes and sh...
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Juan C. Landoni @jclandoni.bsky.social · 21/04/2026
The Landoni Lab opens this summer at UNIL! @fbm-unil.bsky.social 🔬 Quantitative #imaging + systems biology to decipher how #metabolic architecture & #mtDNA dynamically shape tissue development, #aging and #mitodisease. Beyond excited to fire up the lasers, open positions soon! 🧪 #mitochondria #newPI
Landoni lab & UNIL logos, featuring fluorescent images of mitochondria and nematodes
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Satoshi Kawato 川戸智 @kawatosatoshi.bsky.social · 08/03/2026
Big update for #gbdraw! - Multi-record circular plots: Genomes with multiple replicons can now be displayed in a single view! - Advanced linear plots: Focus on regions of interest with granular control over feature selection and color-coding! Try now: gbdraw.app #microbiology #bioinformatics
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Reposted by Florian Fournes
Michael @schlierflab.bsky.social · 15/03/2026
Our newest bioRxiv on the bacterial integron is out (link below). 🧑‍🔬 How it started: Rising #AMR are a challenge for health. A key player is the bacterial integron. Do you remember its recombination efficiency 🧬🧬 correlated with the mechanical stability 💪 of a recombinase-DNA complex? 1/6
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 07/03/2026
Nucleoid-binding protein RicO anchors replication origins to the membrane to ensure correct chromosome segregation in Staphylococcus aureus www.biorxiv.org/content/10.64898/20…
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Justine Collier @justinecollier.bsky.social · 06/02/2026
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience www.cell.com/iscience/ful... 🎊Congrats to my fantastic lab members @noemiematthey.bsky.social , Giorgia Wennubst and Nicolas Pellaton, and to our precious GTF collaborators! 🎉
cell.com
Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein
Properties of biomolecules; Epigenetics; Microbial genomics; Transcriptomics
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Paula Ramiro-Martínez @paularamiro.bsky.social · 27/01/2026
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
pnas.org
Plasmid mutation rates scale with copy number | PNAS
Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...
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Reposted by Florian Fournes
Franklin Nobrega @fnobrega.bsky.social · 17/01/2026
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).
biorxiv.org
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
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Xavier Charpentier @labxc.bsky.social · 13/01/2026
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.
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Wiep Klaas Smits (ExpBac/CMAT) @smitslab.bsky.social · 02/01/2026
A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation www.biorxiv.org/content/10.6...
biorxiv.org
A single DNA methylation site regulates cell fate during Clostridioides difficile sporulation
DNA methylation is a widespread phenomenon in bacteria that can regulate gene expression, although the mechanisms underlying this epigenetic regulation are often poorly understood. In Clostridioides d...
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Reposted by Florian Fournes
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 06/12/2025
Plasmid copy number affects the DNA methylation-driven expression dynamics of the CfrBI restriction-modification system and impacts phage restriction www.biorxiv.org/content/10.64898/20…
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Calum H. G. Johnston @chgjohnston.bsky.social · 26/11/2025
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/...
pnas.org
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...
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Devani Romero Picazo @devaropica.bsky.social · 14/11/2025
Finally out from @daganlab.bsky.social! 🌱🦠🧬 Evolution of the Plant-Associated Pantoea was Accompanied by Plasmid Domestication Events url: academic.oup.com/mbe/article/...
academic.oup.com
Evolution of the Plant-Associated Pantoea was Accompanied by Plasmid Domestication Events
Abstract. Plasmids are important drivers of evolutionary transformations and ecological adaptation in prokaryotes. Plasmids supplying the host with benefic
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 27/10/2025
Fast assembly and in vivo coalescence of ParB biocondensates involved in bacterial DNA partition www.biorxiv.org/content/10.1101/202…
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Ricardo Henriques @henriqueslab.bsky.social · 22/10/2025
🦠🔬🤖🧑‍💻 #mAIcrobe is out! With @pinholab.bsky.social's lab, we launched an open-source framework for high-throughput bacterial image analysis. By rockstars A. Brito & B. Saraiva et al, making #DeepLearning for phenotyping accessible! Easy to use, plus model training 📜 www.biorxiv.org/content/10.1...
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Nature Communications @natcomms.nature.com · 21/10/2025
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
bit.ly
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.
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Florian Roisné-Hamelin @roisnehamelinf.bsky.social · 09/10/2025
Delighted to announce our latest work on how Wadjet loads onto and establishes topological entrapment of plasmid DNA prior to initiating loop extrusion. At @gruberlab.bsky.social, Dubochet Center for Imaging and BSI @igbmc.bsky.social www.cell.com/molecular-ce...
cell.com
Mechanism of DNA entrapment by a loop-extruding Wadjet SMC motor
Wadjet is an SMC-based prokaryotic defense system that eliminates plasmid DNA. Roisné-Hamelin et al. present structures capturing key steps of its DNA-loading mechanism. This work reveals how Wadjet t...
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Justine Collier @justinecollier.bsky.social · 05/09/2025
🤩 Exciting Summer! 🤩 Two of my former postdocs in Switzerland🇨🇭 obtained Lecturer positions (Maîtres de Conférences) in French universities 🇨🇵 : congrats to Antonio Frandi and Florian Fournès !!!! 👏 La relève est assurée! All the best to both of you for this new start. 🤩
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Stephan Gruber @gruberlab.bsky.social · 05/09/2025
Our Wadjet-II paper by @roisnehamelinf.bsky.social is out in polished form: www.cell.com/structure/fu... With a great preview by @kevincorbett.bsky.social & @amardeeep.bsky.social highlighting the potential of Wadjets: Wadjet—Keeping a watchful eye on circular DNA. www.cell.com/structure/fu...
cell.com
Structure of a type II SMC Wadjet complex from Neobacillus vireti
Wadjet are SMC-based prokaryotic defense systems that cleave plasmid DNA. Roisné-Hamelin et al. reconstitute a type II Wadjet and demonstrate that it exhibits substrate selection and cleavage properti...
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Ethan Garner @fleshball.bsky.social · 20/05/2025
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
doi.org
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...
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Wiep Klaas Smits (ExpBac/CMAT) @smitslab.bsky.social · 22/08/2025
The Escherichia coli replication initiator DnaA is titrated on the chromosome www.nature.com/articles/s41...
nature.com
The Escherichia coli replication initiator DnaA is titrated on the chromosome - Nature Communications
A DNA-binding protein, DnaA, regulates the initiation of chromosomal replication in bacteria. Here, Olivi et al. show that the bacterial chromosome sequesters DnaA in a growth rate-dependent manner, s...
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Didier Mazel @amazeld.bsky.social · 20/08/2025
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...
sciencedirect.com
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…
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Javier Santoyo @jsantoyo.bsky.social · 16/08/2025
Giant extrachromosomal element “Inocle” potentially expands the adaptive capacity of the human oral microbiome. #BacterialExtrachromosomalElements #OralMicrobiome @natcomms.nature.com 🧬 www.nature.com/articles/s41...
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Shraddha Shitut @shetoot.bsky.social · 04/03/2025
Excited to share our paper published in @currentbiology.bsky.social that explores the consequences of having multiple genomes in a bacterial model system and it’s benefits in a multidrug environment ! www.cell.com/current-biol...
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lizzthrall.bsky.social @lizzthrall.bsky.social · 05/08/2025
Excited to share another study from my lab @fordhamchem now out @narjournal.bsky.social‬: doi.org/10.1093/nar/.... Most bacterial DNA polymerases must interact with the sliding clamp DnaN for their function, but we show that it’s more complicated in B. subtilis DNA replication. (1/4)
doi.org
The B. subtilis replicative polymerases bind the sliding clamp with different strengths to tune their activity in DNA replication
Abstract. Ring-shaped sliding clamp proteins are essential components of the replication machinery across all domains of life. DNA polymerases bind the cla
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Florian Fournes @flofournes.bsky.social · 28/07/2025
One of the best places to conduct scientific research with a wonderfull project and a great PI!!
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Daniela Barillà @danielabarilla.bsky.social · 22/07/2025
And the story is published now!🍾 www.nature.com/articles/s41... Open access link: rdcu.be/exnOc Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏 #microsky #archaeasky
nature.com
Coupling chromosome organization to genome segregation in Archaea - Nature Communications
Proteins SegA and SegB are important for chromosome segregation and organization in archaea of the order Sulfolobales, but mechanisms are unclear. Here, Kabli et al. uncover patterns and mechanisms th...
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Jesse Shapiro @bjesseshapiro.bsky.social · 01/07/2025
One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial: Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp). www.nature.com/articles/s41... (1/n)
nature.com
Prevalent chromosome fusion in Vibrio cholerae O1 - Nature Communications
The pathogenic bacterium Vibrio cholerae typically has two circular chromosomes. Here, Cuénod et al. analyse 467 clinical isolates and identify several independent chromosome fusion events that are li...
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Matthew Cobb @matthewcobb.bsky.social · 26/06/2025
Just learned that Frank Stahl (of the Meselson and Stahl DNA replication experiment ("the most beautiful experiment in biology") died at the beginning of April, to no fanfare. Here's a lovely video of them reminiscing: www.youtube.com/watch?v=7-tn...
youtube.com
The Most Beautiful Experiment: Meselson and Stahl
YouTube video by Science Communication Lab
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Pierre Dupuy @pierredupuy.bsky.social · 12/06/2025
After a PhD and two postdocs, I’m very proud to be joining the CNRS as a Chargé de recherche, this is a meaningful milestone. Huge thanks to Claude Bruand, @michaelglickman.bsky.social, and @oneyrolles.bsky.social for their guidance and support. Olivier, let’s turn this into exciting discoveries!
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Jan-Willem Veening @veeninglab.com · 10/06/2025
New tenure track assistant professor position in molecular microbiology in our department @dmf-unil.bsky.social @unil.bsky.social! We are casting a wide net for an experimental molecular microbiologist. Apply here: wwwfbm.unil.ch/releve/appli...
wwwfbm.unil.ch
DMF: Tenure Track Assistant Professor towards Associate Professor in Molecular Microbiology - Site des postulations FBM
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Céline Loot @celineloot.bsky.social · 22/05/2025
www.pasteur.fr/fr/journal-r...
pasteur.fr
Les bactéries utilisent les mêmes outils pour résister aux antibiotiques et aux virus
La résistance des bactéries aux antibiotiques est un phénomène qui s’accentue, créant un problème de santé publique majeur. Parmi les possibles alternatives aux antibiotiques, l’utilisation de virus i...
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 21/05/2025
Marie Curie fellowship, post-doc hosting oppotunity in my lab. MSCA Post-doctoral Fellowship at IBPC Paris on RNA modifications in bacteria (FRANCE) 🦠💫 euraxess.ec.europa.eu/jobs/hosting...
euraxess.ec.europa.eu
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Céline Loot @celineloot.bsky.social · 09/05/2025
At least 10% of the V. cholerae integron cassettes have novel antiphage activities (see below). Considering that there are 25,000 distinct cassettes of unknown function, integrons constitute an extraordinary and almost inexhaustible reservoir of antiphage functions!
science.org
Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing, and shuffling gene cassettes. While mobile integrons are well known for spreading antibiotic resistance genes, t...
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Baptiste Darracq @baptistedarracq.bsky.social · 09/05/2025
White smoke, we have a new pope and also 16 new anti-phages systems in sedentary integrons (SCIs) ! In collaboration with the Rocha lab, we show in our new paper that cassettes of these large platforms encode many known anti-phage defenses, and uncovered 16 new ones. www.science.org/doi/10.1126/...
science.org
Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing, and shuffling gene cassettes. While mobile integrons are well known for spreading antibiotic resistance genes, t...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 27/04/2025
Biofilm architecture determines the dissemination of conjugative plasmids #PNAS from @sbigot.bsky.social, @knutdrescher.bsky.social labs www.pnas.org/doi/10.1073/...
pnas.org
Biofilm architecture determines the dissemination of conjugative plasmids | PNAS
Plasmid conjugation is a contact-dependent horizontal gene transfer mechanism that significantly contributes to the dissemination of antibiotic res...
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Nathan Fraikin @nfrk92.bsky.social · 23/04/2025
Our set of new prokaryote-optimized fluorescent proteins is now published ! #microbiology #microsky #microscopy 🧫🦠🔬 www.science.org/doi/10.1126/...
science.org
A palette of bright and photostable monomeric fluorescent proteins for bacterial time-lapse imaging
Bright and photostable monomeric fluorescent proteins enable long-term time-lapse imaging in E. coli.
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Jan-Willem Veening @veeninglab.com · 23/04/2025
Now online @narjournal.bsky.social academic.oup.com/nar/article/...
academic.oup.com
HU promotes higher order chromosome organization and influences DNA replication rates in Streptococcus pneumoniae
Abstract. Nucleoid-associated proteins (NAPs) are crucial for maintaining chromosomal compaction and architecture, and are actively involved in DNA replica
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MV Mazzuoli @mvmazzuoli.bsky.social · 23/04/2025
OUT NOW! 👇🏼We built a make-or-break Prime editing tool—have a read to discover how it’s changing the way we do genomic engineering. www.nature.com/articles/s41... @JWVeening @AxelJans & all others authors! 👏🏻
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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 22/03/2025
Cytosine methylation by ScmA contributes to the fitness of Caulobacter crescentus cells naturally expressing a Vsr-like protein www.biorxiv.org/content/10.1... Another orphan cytosine methyltransferase in bacteria #microsky
biorxiv.org
Cytosine methylation by ScmA contributes to the fitness of Caulobacter crescentus cells naturally expressing a Vsr-like protein
While methylated cytosines are known to play important roles in eukaryotes, their significance in bacteria remains poorly understood especially when they are added on genomes by DNA methyltransferases...
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Stephan Gruber @gruberlab.bsky.social · 11/03/2025
Happy to share the beautiful structure of a Wadjet SMC complex by @roisnehamelinf.bsky.social, with support from the DCI and @drhonsworth.bsky.social ! This is a type II Wadjet with unique characteristics including a tandem KITE subunit, distinct coiled coil architecture and a deviant hinge.
Side view of the structure of a monomer of type II Wadjet.
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 25/02/2025
Linear dicentric chromosomes in bacterial natural isolates reveal common constraints for replicon fusion www.biorxiv.org/content/10.1101/202…
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