Fanny DEMAY

#Ribosome #RNASky Aged ribosomes do not elongate well on positively charged residues

🧬✏️ RNA Modifications Newsletter - March 2026 issue #9

RNA modifications are not static decorations, they are dynamic regulatory determinants. 🦠 The RNA modifications newsletter for March is out 👉https://rnamodifupdates.substack.com/p/rna-modifications-newsletter-march

Revitalizing actinobacteria research: an urgent response to the antimicrobial resistance crisis - Natural Products and Bioprospecting Abstract The crisis of antimicrobial resistance (AMR) is escalating while the antibiotic pipeline remains stagnant. Our bibliometric analysis of eight decades of literature reveals a critical imbalanc...

Research into filamentous actinomycetes, the antibiotic producers, is in steep decline. Loads of natural products chemistry research worldwide but not much aimed at understanding their biology and ecology. The latter is key to unlocking their specialised metabolism

link.springer.com/article/10.1...

ADAM-tRNA-seq: an optimized approach for demultiplexing and enhanced hierarchal mapping in direct tRNA sequencing Abstract. Transfer RNAs (tRNAs) play an essential role in protein synthesis and cellular homeostasis, and their dysregulation is associated with various hu

Interested in direct tRNA-seq by Nanopore? We developed a new RNA-based barcoding aproach for seq parallelization; it is also cost-saving. Scripts available on github. #tRNA #Nanopore

track.smtpsendmail.com/9032119/c?p=...

Proč dal mikrobiolog Rufin Kouipou přednost Česku před Japonskem? V rámci MERIT hledá v @mbuavcr.bsky.social nová antibiotika. 🦠 Rufin vysvětluje, proč je pro vědce stabilita důležitější než prestižní, ale krátká stipendia. Oceňuje českou otevřenost i přímočarost.

👉 bit.ly/4qFHixF

We’re thrilled to share our latest iTP-seq protocol for mapping bacterial translation landscapes in vitro — with a complete experimental workflow streamlined by Mélanie Gillard and an open source Python library for data analysis developed by Thibaud Renault.

🦠 Is life in the universe rare, or might it occur almost everywhere? The PROTOCELL project led by Dr. Klára Hlouchová at IOCB Prague aims to find out. 1/2

#UOCHB #IOCB #IOCBPrague #AVCR #IOCB2025

In vivo development of elevated linezolid resistance mediated by a deletion in ribosomal protein L3 in clinical Enterococcus faecium | Antimicrobial Agents and Chemotherapy Linezolid (LZD) is an important clinical option for treating serious gram-positive infections, especially multidrug-resistant strains such as methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, and multidrug-resistant Streptococcus pneumoniae (1, 2). It exerts its antibacterial effect by binding to the ribosomal peptidyl transferase center (PTC) of the 50S subunit, thereby inhibiting bacterial protein synthesis. However, shortly after its introduction into clinical use in 2000, LZD-resistant strains emerged from clinical Enterococcus faecium and Staphylococcus aureus (3, 4) and subsequently were reported in coagulase-negative staphylococci (5) and other species (6).

In vivo development of elevated linezolid resistance mediated by a deletion in ribosomal protein L3 in clinical Enterococcus faecium | Antimicrobial Agents and Chemotherapy journals.asm.org/doi/10.1128/...

Hypoxia-induced ribosomal RNA modifications in the peptidyl-transferase center contribute to anaerobic growth of bacteria Ishiguro et al. identify stereoselective ribose-backbone methylations in the peptidyl-transferase center of E. coli ribosomes, installed by the cobalamin-dependent enzyme RlmX. These methylations, tog...

Hypoxia-induced ribosomal RNA modifications in the peptidyl-transferase center contribute to anaerobic growth of bacteria: Molecular Cell www.cell.com/molecular-ce...

After D2449 by rdsA, now new methylations in E.coli rRNA under stress 💫

Deep learning speeds the search for new antibiotic scaffolds - Nature Biotechnology A deep learning model trained on experimental data from high-throughput screening identifies structurally novel antimicrobial compounds.

A deep learning model trained on experimental data from high-throughput screening identifies structurally novel antimicrobial compounds #NBTNV go.nature.com/47fxSSv
rdcu.be/eSIvL

Using "in extracto cryo-EM", we visualize ribosomes in mammalian lysates, including RRL. "Hibernating" ribosomes carry an extended set of proteins that protect functional centers. These include elongation factor eEF2, LARP1 implicated in mTOR signaling, eIF5A etc. www.biorxiv.org/content/10.1...

🦠 Is life in the universe rare, or might it occur almost everywhere?

The PROTOCELL project by @hlouchova-lab.bsky.social in collab with @pluskal-lab.org and with support of @esa.int aims to find out ► www.uochb.cz/en/news/742/...

#IOCB #IOCBPrague #AVCR #chemie #chemistry #czechscience

‼️🚨🗓️ CONTAMCALENDAR 2026 🗓️🚨‼️

Excited to say the ContamCalendar is back for its fifth edition! We’ve created a fresh new design, folding out for an A3 monthly spread. It’s our best yet, we hope you’ll love it 🗓️🦠🧫🍄

Get yours here ➡️ www.contam.club ⬅️

chris hill PhD Projects, Programmes & Scholarships - 3 PhDs Listed FindAPhD. Search Funded PhD Projects, Programmes & Scholarships in chris hill. Search for PhD funding, scholarships & studentships in the UK, Europe and around the world.

🚨Attention prospective PhD students🚨
Are you interested in molecular mechanisms, RNA viruses, structural biology or biophysics? 🧬🦠🧪

We have THREE fully-funded PhD projects available for October 2026 entry:
www.findaphd.com/phds/?Keywor...

Please share/repost, and get in touch if you're interested

Many nice #RNA & #ribosome papers in the latest issue of @narjournal.bsky.social 🦠💫 academic.oup.com/nar/issue/53...
⬇️links in comments

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...

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

Job advertisement

We are hiring…position suitable for PhD student with interest in ribosomes, antibiotics and cryoEM…
www.uni-hamburg.de/en/stellenan...

Oxidative stress sensing by the translation elongation machinery promotes production of detoxifying selenoproteins Selenocysteine, incorporated into polypeptides at recoded termination codons, plays an essential role in redox biology. Using GPX1 and GPX4, selenoenzymes that mitigate oxidative stress, as reporters,...

Colliding ribosomes are potent signals of cellular stress. But do cells use ‘programmed’ ribosome collisions to regulate gene expression? I’m excited to present a new story from my lab led by Frederick Rehfeld(@fred-rehfeld.bsky.social) which revealed that the answer is YES! Read on to find out how👇

Our method paper to produce efficient cell-free translation lysates from diverse human cell types is out 🎉 www.jbc.org/article/S002... @unibe.ch @mcid-unibe.bsky.social
@muehlemann.bsky.social @nickkouvelas.bsky.social

A human cell-free translation screen identifies the NT-2 mycotoxin as a ribosomal peptidyl transferase inhibitor Translation inhibitors are invaluable for probing ribosome function and therapeutic applications, but systematic discovery in human systems is limited by the lack of scalable, screening-compatible cel...

🚀 New preprint!
We used a human cell-free translation screen (~28 000 compounds) to discover NT-2, a #Fusarium -derived #mycotoxin that blocks human ribosomes.
#Cryo-EM at 1.72 Å reveals a link between chemical inhibition and ribosome dormancy.
www.biorxiv.org/content/10.1...

Mycobacterial TrmI (m¹A58) is linked to aminoglycoside tolerance. Ribosomes stall in an alanine-rich region that controls whiB7, and trans-translation increases this stalling, keeping WhiB7 active and helping mycobacteria survive antibiotic stress.🦠#rnasky => preprint www.biorxiv.org/content/10.1...

#ribosome #RNASky 🧪 eukaryotic ribosome-specific inhibitor associated w ribosome dormancy

Dvě vědkyně z @mbuavcr.bsky.social - Natalia Slonská a Lucie Najmanová, se zúčastnily soutěže Věda fotogenická, kterou pořádá @akademievedcr.bsky.social. Do soutěže přihlásily snímky, které propojují krásu květu fuchsie se světem půdních bakterií Streptomyces coelicolor.

Protein Domain Designer tool for the generation of publication-ready protein domain diagrams

New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com

Structural insights into YheS-mediated release of SecM-arrested ribosome. ATPase-binding cassette subfamily F (ABCF) proteins interact with the ribosome to resolve translation defects near the peptidyl-transferase center, induced by ribosome-targeting antibiotics or "hard-t...

Structural insights into YheS-mediated release of SecM-arrested ribosome. www.biorxiv.org/content/10.1... 🦠 #ribosome #rnasky

Here, we show that bacterial ribosomes—often viewed as conserved drug targets—actually vary across species due to extensive sequence variation in their drug-binding residues. In some cases, this divergence may lead to intrinsic drug resistance in certain bacterial clades: doi.org/10.1016/j.ce...

Happy to share a new paper from our lab with my little contribution! 🥳🥳🥳
We show that antibiotic resistance ABC-F proteins fine-tune responses to ribosome-binding antibiotics. Thanks to ABC-Fs, bacteria can differentiate between antibiotic classes and even concentrations for a tailored response. 🦠💊⬇️

ABCF protein-mediated resistance shapes bacterial responses to antibiotics based on their type and concentration | mBio Bacteria adapt to diverse stimuli mainly through transcriptional changes that regulate adaptive protein factors. Here, we show that responses to protein synthesis-inhibiting antibiotics are fine-tuned by antibiotic resistance ABCF proteins at the ...

New ABCF article from @balikovalab.bsky.social group!

Even though ABCF proteins have the same shape and act on the ribosome E-site, they have very different role in bacteria physiology level.

What an interesting topic!🤩

doi.org/10.1128/mbio...

#rnasky #microsky