Zeynep Baharoglu
zeynepbaharoglu.bsky.social
Zeynep Baharoglu
@zeynepbaharoglu.bsky.social
RNA modifications, antibiotic tolerance, bacterial stress, non coding RNAs, Vibrio cholerae.
Institut Pasteur & EGM (IBPC, CNRS)
drug-specific ribosome stall signatures after short antibiotic exposure can predict long-term growth inhibition, i.e., phenotypic AMR. => detected by s5PSeq degradome-sequencing🦠 #AMR doi.org/10.1101/2025...
A streamlined nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing
Antimicrobial resistance (AMR) poses a significant threat to public health. Rapid and accurate antimicrobial sensitivity testing is essential to guide effective treatment. Here, we present “simplified...
doi.org
November 25, 2025 at 1:40 PM
Reposted by Zeynep Baharoglu
Our paper is out! Analysis of 30K+ genomes revealed that CPR bacteria assemble their ribosomes in unconventional ways, and that these assembly processes appear to have co-evolved with ribosome structure. doi.org/10.1093/molb... #Ribosome #Evolution #Patescibacteria #MBE
November 24, 2025 at 1:15 PM
Reposted by Zeynep Baharoglu
Evolutionary Flexibility of Ribosome Biogenesis in Bacteria | Molecular Biology and Evolution | Oxford Academic https://academic.oup.com/mbe/article/42/11/msaf288/8340222?login=false
Evolutionary Flexibility of Ribosome Biogenesis in Bacteria
Abstract. Ribosomes are essential for protein synthesis and require ribosome biogenesis factors for assembly. To uncover the evolutionary diversity of ribo
dx.doi.org
November 24, 2025 at 10:45 AM
Reposted by Zeynep Baharoglu
#MicroSky #RNASky & ribosomologists + chromosome segregationists of all colors take note 👇
The role of active mRNA–ribosome dynamics and closing constriction in daughter chromosome separation in Escherichia coli
doi.org/10.1073/pnas...
November 14, 2025 at 1:31 PM
Reposted by Zeynep Baharoglu
Structural insights into the chaperone role of uncharged tRNA(Arg/Gln) in viral RNAP assembly #RNASky 🧪 www.nature.com/articles/s41...
tRNA as an assembly chaperone for a macromolecular transcription-processing complex - Nature Structural & Molecular Biology
Here, the authors solve a series of cryo-electron microscopy structures that show how transfer RNAs (tRNAs) can guide the assembly of the multisubunit poxvirus RNA polymerase, uncovering a role of tRN...
www.nature.com
November 15, 2025 at 9:44 PM
Reposted by Zeynep Baharoglu
Not all RelE toxins are created equally. RelE1, E2 cut 16S rRNA, RelE3 degrades mRNA in a ribosome-dependent manner. #MicroSky #Ribosome 🧪 #RNASky ⬇️
Two M. tuberculosis RelE toxins don’t cut mRNA, they slice 16S rRNA itself, shutting down translation in a totally unexpected way, new study reveals.
A big leap in understanding TB’s survival tricks and new angles for therapies.

📖 shorturl.at/Z8MVX
✍️ @genevauxpierre.bsky.social & coll.
#MicroSky
November 18, 2025 at 6:56 PM
Many nice #RNA & #ribosome papers in the latest issue of @narjournal.bsky.social 🦠💫 academic.oup.com/nar/issue/53...
⬇️links in comments
November 12, 2025 at 7:58 PM
Reposted by Zeynep Baharoglu
genome-wide CRISPRi screens to map how uropathogenic E. coli (UPEC) survives in human urine 🦠 #AMR #UTI
Genome-scale CRISPRi profiling reveals metabolic vulnerabilities of uropathogenic Escherichia coli in human urine
Urinary tract infections (UTIs) are among the most common infectious diseases, causing over 400 million cases and 260,000 deaths annually. Women are disproportionately affected, with ∼50% experiencing...
www.biorxiv.org
November 7, 2025 at 4:19 PM
Reposted by Zeynep Baharoglu
Next Codon Usage Meeting, May 31st to June 3rd, 2026 in Montreal right after the RNA Society Meeting. The list of speakers will be up soon.

sites.google.com/view/codonus...
codon usage
About the Conference Codon usage bias—the preference for certain synonymous codons—is a key factor in genome regulation. Codon usage and synonymous codon mutations have been shown to influence gene ex...
sites.google.com
November 5, 2025 at 10:55 PM
and the English version. Thanks @pasteur.fr for highlighting this study. 🦠 #AMR
November 7, 2025 at 7:02 AM
The authors explore targeting intrinsic resistance mechanisms (those built into bacterial physiology rather than acquired resistance genes) in Escherichia coli, to both sensitize bacteria to antibiotics and reduce their ability to evolve new resistance 🦠 #AMR dx.plos.org/10.1371/jour...
Impeding pathways of intrinsic resistance in Escherichia coli confers antibiotic sensitization and resistance proofing
Intrinsic resistance pathways in E. coli can be exploited to enhance antibiotic sensitivity and limit resistance evolution. This study shows that genetic inhibition of efflux pumps and cell envelope b...
dx.plos.org
November 5, 2025 at 9:54 AM
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
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...
journals.plos.org
November 3, 2025 at 11:58 PM
🎃 Trick or transcript?
Bacteria rewire their RNA world under stress & infection. tRNA mods as dual-function sensors, phage tRNA slashers, hibernating ribosomes & haunted translation hubs.
🧬🧪 Full November 1st issue → #RNAmod #Epitranscriptomics #HalloweenScience
#rnasky #microsky
📰 🎃 RNA Modifications Newsletter – October 31st - November 1st, 2025
Issue #5
rnamodifupdates.substack.com
October 31, 2025 at 8:14 PM
🦠💊 L’Institut @pasteur.fr vient de publier un communiqué de presse sur nos récents travaux, qui décrivent une nouvelle piste pour augmenter l’efficacité des antibiotiques. #Pasteurdon #Recherche #Science #AMR

Merci à toutes celles et ceux qui ont contribué.

📘 English version coming soon!
Une piste prometteuse pour augmenter l’efficacité des antibiotiques
Les aminosides sont des antibiotiques efficaces contre de très nombreuses bactéries telles que Escherichia coli, Pseudomonas aeruginosa ou Staphylococcus aureus. Mais jusqu’à présent, personne ne sava...
www.pasteur.fr
October 31, 2025 at 10:37 AM
Reposted by Zeynep Baharoglu
🚨 #RNAsky 🚨
October 26, 2025 at 6:02 PM
EF-G variants (fusA mutants) slow down ribosome translocation only when the ribosome is bound by an aminoglycoside => the antibiotic isn’t displaced, but translation on that ribosome is effectively stalled 🦠 rdcu.be/eNt96
Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides
Nature Communications - Mutations in elongation factor G protect bacteria from aminoglycoside antibiotics through unknown mechanisms. Here, the authors show that the mutations selectively slow the...
rdcu.be
October 30, 2025 at 1:10 PM
Reposted by Zeynep Baharoglu
🧬 New review on nanopore basecalling models is out! ✨
Congrats to @soniacruciani.bsky.social (former Novoa Lab PhD, now postdoc at the Deplancke Lab, EPFL) and @evamarianovoa.bsky.social👏
📖 www.nature.com/articles/s41...
Client Challenge
www.nature.com
October 14, 2025 at 12:28 PM
Nucleoid structure and dynamics influence natural chromosomal transformation in Bacillus subtilis: the role of EbfC url: academic.oup.com/nar/article/...
Nucleoid structure and dynamics influence natural chromosomal transformation in Bacillus subtilis: the role of EbfC
Abstract. Natural chromosomal transformation (NCT) in Bacillus subtilis requires RecA and its accessory proteins including RecX and RecD2. Inactivation of
academic.oup.com
October 25, 2025 at 12:10 PM
MazF endoribonuclease promotes resolution of transcription–replication conflicts at ribosomal RNA genes in Escherichia coli url: academic.oup.com/nar/article/...
MazF endoribonuclease promotes resolution of transcription–replication conflicts at ribosomal RNA genes in Escherichia coli
Abstract. Toxins from toxin–antitoxin (TA) systems, widely distributed genetic elements in prokaryotic genomes, are traditionally viewed as growth inhibito
academic.oup.com
October 25, 2025 at 12:04 PM