Jonathan Jagodnik
@jagodnikscience.bsky.social
RNA! RNA, everywhere! (Same could be said about bacteria...)
Research Associate at RNA control of gene expression lab, Microbial Gene Expression, IBPC - CNRS.
Research Associate at RNA control of gene expression lab, Microbial Gene Expression, IBPC - CNRS.
Pinned
30S-seq redefines the bacterial Ribosome Binding Site
The translation initiation step is rate limiting for the efficiency of gene expression in all organisms. However, the mechanism of ribosome recruitment to mRNA start sites strikingly differs between e...
www.biorxiv.org
I am thrilled to share this new preprint from our lab!
We find (>800!) 30S binding sites in hundreds of 5'UTRs, but also new dynamic steps of translation initiation.
www.biorxiv.org/content/10.1...
Congrats to all co-authors at the RNA control of gene expression lab, IBPC CNRS
(Thread, 1/6)
We find (>800!) 30S binding sites in hundreds of 5'UTRs, but also new dynamic steps of translation initiation.
www.biorxiv.org/content/10.1...
Congrats to all co-authors at the RNA control of gene expression lab, IBPC CNRS
(Thread, 1/6)
Reposted by Jonathan Jagodnik
Our latest paper on protein expression and mRNA stability is out!
academic.oup.com/nar/article/...
Check out how to increase your protein output with a simple trick.
Congratulations to first author @Anna Lipońska, it was a great collaboration with the Aalberts group.
#RNAsky #ribosome #EGM
academic.oup.com/nar/article/...
Check out how to increase your protein output with a simple trick.
Congratulations to first author @Anna Lipońska, it was a great collaboration with the Aalberts group.
#RNAsky #ribosome #EGM
Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli
Abstract. Protein synthesis efficiency is highly dependent on the messenger RNA (mRNA) coding sequence. Furthermore, there is extensive evidence of a corre
academic.oup.com
December 23, 2025 at 10:29 AM
Our latest paper on protein expression and mRNA stability is out!
academic.oup.com/nar/article/...
Check out how to increase your protein output with a simple trick.
Congratulations to first author @Anna Lipońska, it was a great collaboration with the Aalberts group.
#RNAsky #ribosome #EGM
academic.oup.com/nar/article/...
Check out how to increase your protein output with a simple trick.
Congratulations to first author @Anna Lipońska, it was a great collaboration with the Aalberts group.
#RNAsky #ribosome #EGM
Reposted by Jonathan Jagodnik
🫳 Metastable folding of Bacillus subtilis glmS ribozyme modulates turnover by RNase J1:
www.sciencedirect.com/science/arti...
#subtiwiki
www.sciencedirect.com/science/arti...
#subtiwiki
Metastable folding of Bacillus subtilis glmS ribozyme modulates turnover by RNase J1
Rapid turnover of glmS mRNA in Bacillus subtilis by 5′-3’ exoribonuclease RNase J is essential for feedback regulation of glucosamine-6-phosphate (Glc…
www.sciencedirect.com
December 27, 2025 at 7:38 AM
🫳 Metastable folding of Bacillus subtilis glmS ribozyme modulates turnover by RNase J1:
www.sciencedirect.com/science/arti...
#subtiwiki
www.sciencedirect.com/science/arti...
#subtiwiki
Reposted by Jonathan Jagodnik
In this study, we highlight the importance of the base composition of the first codons for protein expression. An increased abundance of adenine (A) and a decrease in guanine (G) enhance expression and improve mRNA stability. The mediator of this effect is the ribosome.
Our latest paper on protein expression and mRNA stability is out!
academic.oup.com/nar/article/...
Check out how to increase your protein output with a simple trick.
Congratulations to first author @Anna Lipońska, it was a great collaboration with the Aalberts group.
#RNAsky #ribosome #EGM
academic.oup.com/nar/article/...
Check out how to increase your protein output with a simple trick.
Congratulations to first author @Anna Lipońska, it was a great collaboration with the Aalberts group.
#RNAsky #ribosome #EGM
Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli
Abstract. Protein synthesis efficiency is highly dependent on the messenger RNA (mRNA) coding sequence. Furthermore, there is extensive evidence of a corre
academic.oup.com
December 23, 2025 at 10:31 AM
In this study, we highlight the importance of the base composition of the first codons for protein expression. An increased abundance of adenine (A) and a decrease in guanine (G) enhance expression and improve mRNA stability. The mediator of this effect is the ribosome.
Reposted by Jonathan Jagodnik
Are authors fairly judged by assessing the #journals in which their work is published? @bihutchins.bsky.social &co reveal that most influential papers are published in lower tier journals, and more authors would be better recognized with #ArticleLevelMetrics #ALMs @plosbiology.org 🧪 plos.io/4oV58Ed
December 17, 2025 at 5:30 PM
Are authors fairly judged by assessing the #journals in which their work is published? @bihutchins.bsky.social &co reveal that most influential papers are published in lower tier journals, and more authors would be better recognized with #ArticleLevelMetrics #ALMs @plosbiology.org 🧪 plos.io/4oV58Ed
DusB links tRNA modification with oxydative stress response in V. cholerae! Congrats to @zeynepbaharoglu.bsky.social and colleagues!
Our new paper on DusB’s role in redox metabolism in V. cholerae is now out in @narjournal.bsky.social linking tRNAmodif enzymes and metabolic adaptation.
Beyond RNA modification: a tRNA-modifying enzyme shaping oxidative stress resilience and metabolism in V. cholerae #rnasky #rnabiology
😊🦠💫
Beyond RNA modification: a tRNA-modifying enzyme shaping oxidative stress resilience and metabolism in V. cholerae #rnasky #rnabiology
😊🦠💫
Beyond RNA modification: a novel role for tRNA modifying enzyme in oxidative stress response and metabolism
Abstract. RNA modifications play a fundamental role in regulating essential cellular processes, including translation fidelity and stress adaptation. While
academic.oup.com
December 15, 2025 at 11:43 AM
DusB links tRNA modification with oxydative stress response in V. cholerae! Congrats to @zeynepbaharoglu.bsky.social and colleagues!
Reposted by Jonathan Jagodnik
RNA–RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA–mRNA pairing url: academic.oup.com/nar/article/...
RNA–RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA–mRNA pairing
Abstract. Most bacterial small regulatory RNAs (sRNAs) modulate gene expression by forming complementary base pairs with target messenger RNAs (mRNAs), dep
academic.oup.com
December 14, 2025 at 4:06 AM
RNA–RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA–mRNA pairing url: academic.oup.com/nar/article/...
An rRNA modification to adapt translation to anaerobic conditions!
Online Now: Hypoxia-induced ribosomal RNA modifications in the peptidyl-transferase center contribute to anaerobic growth of bacteria Online now:
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, together with ho5C2501, are specifically induced under hypoxia. The hypoxia-induced modifications activate ribosomes, enhancing translational capacity and thereby promoting bacterial fitness in anaerobic conditions.
dlvr.it
December 10, 2025 at 9:30 PM
An rRNA modification to adapt translation to anaerobic conditions!
Reposted by Jonathan Jagodnik
The EMBO Gold Medal 2025 was awarded to Tanmay Bharat and David Bikard: https://www.embo.org/press-releases/embo-gold-medal-2025-awarded-to-tanmay-bharat-and-david-bikard/ 🧪
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
December 10, 2025 at 1:40 PM
The EMBO Gold Medal 2025 was awarded to Tanmay Bharat and David Bikard: https://www.embo.org/press-releases/embo-gold-medal-2025-awarded-to-tanmay-bharat-and-david-bikard/ 🧪
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.
Exametabolomics!
Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch
Teaser: Increased proline in ΔputP
#microsky #MEvoSky
Teaser: Increased proline in ΔputP
#microsky #MEvoSky
December 7, 2025 at 9:29 PM
Exametabolomics!
Reposted by Jonathan Jagodnik
Today, Minister-President Markus Söder awarded @jorg-vogel-lab.bsky.social the Bavarian Maximilian Order. Presented every two years, the award recognizes outstanding accomplishments in science & the arts and is regarded as one of the state’s highest honors. Congrats on the “Bavarian Nobel Prize”! 👏🎉
December 3, 2025 at 3:04 PM
Today, Minister-President Markus Söder awarded @jorg-vogel-lab.bsky.social the Bavarian Maximilian Order. Presented every two years, the award recognizes outstanding accomplishments in science & the arts and is regarded as one of the state’s highest honors. Congrats on the “Bavarian Nobel Prize”! 👏🎉
Very cool paper, studying mechanisms (and a toxin) targeting the ribosome, translation initiation and the use of Shine-Dalgarno motifs!
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
A big leap in understanding TB’s survival tricks and new angles for therapies.
📖 shorturl.at/Z8MVX
✍️ @genevauxpierre.bsky.social & coll.
#MicroSky
November 19, 2025 at 12:24 PM
Very cool paper, studying mechanisms (and a toxin) targeting the ribosome, translation initiation and the use of Shine-Dalgarno motifs!
Reposted by Jonathan Jagodnik
BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:
October 11, 2025 at 2:10 AM
BREAKING: Friday night massacre underway at CDC. Doznes of "disease detectives," high-level scientists, entire Washington staff and editors of the MMWR (Morbidity and Mortality Weekly Report) have all been RIFed and received the following notice:
Reposted by Jonathan Jagodnik
Open position to work on Type IX secretion (#T9SS) in our lab, in collaboration withe the group of Eric Reynolds at the Dental School of the University of Melbourne. Please spread the word, and forward to anyone potentially interested ! Apply here:
emploi.cnrs.fr/Offres/Docto...
emploi.cnrs.fr/Offres/Docto...
Portail Emploi CNRS - Offre d'emploi - Thèse en Microbiologie-Biochimie (H/F)
emploi.cnrs.fr
October 9, 2025 at 12:18 PM
Open position to work on Type IX secretion (#T9SS) in our lab, in collaboration withe the group of Eric Reynolds at the Dental School of the University of Melbourne. Please spread the word, and forward to anyone potentially interested ! Apply here:
emploi.cnrs.fr/Offres/Docto...
emploi.cnrs.fr/Offres/Docto...
Reposted by Jonathan Jagodnik
Two group leader positions available in the broader areas of RNA science, RNA technologies, and RNA medicine. Attractive packages and a great environment. Come and join us at Helmholtz RNA Würzburg, Bavaria.
October 8, 2025 at 9:45 PM
Two group leader positions available in the broader areas of RNA science, RNA technologies, and RNA medicine. Attractive packages and a great environment. Come and join us at Helmholtz RNA Würzburg, Bavaria.
Reposted by Jonathan Jagodnik
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
September 15, 2025 at 5:26 PM
hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!
Reposted by Jonathan Jagodnik
Communiqué de presse : financement de la recherche publique : la communauté scientifique alerte sur un système à bout de souffle. #veilleESR, @info.gouv.fr @agencerecherche.bsky.social @cnrs.fr @franceuniversites.bsky.social @inserm.fr @inrae-france.bsky.social @enseignementsup-recherche.gouv.fr
September 15, 2025 at 11:41 AM
Communiqué de presse : financement de la recherche publique : la communauté scientifique alerte sur un système à bout de souffle. #veilleESR, @info.gouv.fr @agencerecherche.bsky.social @cnrs.fr @franceuniversites.bsky.social @inserm.fr @inrae-france.bsky.social @enseignementsup-recherche.gouv.fr
Congrats to @mlejars.bsky.social for this really cool publication!
Tired of your somewhat easy life doing genetics in E.coli? Make it even way easier with Maxence's method!!
Tired of your somewhat easy life doing genetics in E.coli? Make it even way easier with Maxence's method!!
Happy to share the published version of our genetic toolbox, EASY-edit, for simple, flexible and efficient targeted editing in E. coli!
Feel free to to try it, we can send strains and plasmids!
academic.oup.com/nar/article/...
Feel free to to try it, we can send strains and plasmids!
academic.oup.com/nar/article/...
EASY-edit: a toolbox for high-throughput single-step custom genetic editing in bacteria
Abstract. Targeted gene editing can be achieved using CRISPR–Cas9-assisted recombineering. However, high-efficiency editing requires careful optimization f
academic.oup.com
September 10, 2025 at 1:28 PM
Congrats to @mlejars.bsky.social for this really cool publication!
Tired of your somewhat easy life doing genetics in E.coli? Make it even way easier with Maxence's method!!
Tired of your somewhat easy life doing genetics in E.coli? Make it even way easier with Maxence's method!!
Reposted by Jonathan Jagodnik
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!
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.
www.science.org
September 6, 2025 at 9:35 AM
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!
Reposted by Jonathan Jagodnik
Exciting FULL PROFESSORSHIP at the Vienna BioCenter - Molecular Mechanisms of Disease Mechanisms: www.maxperutzlabs.ac.at/news/open-po... Come be our colleague!
Full Professorship in Molecular Mechanisms of Disease
The Max Perutz Labs - one of Europe’s leading institutes for basic research in the life sciences - invite applications for a Full Professorship in Molecular Mechanisms of Disease. We are seeking outst...
www.maxperutzlabs.ac.at
September 4, 2025 at 10:25 AM
Exciting FULL PROFESSORSHIP at the Vienna BioCenter - Molecular Mechanisms of Disease Mechanisms: www.maxperutzlabs.ac.at/news/open-po... Come be our colleague!
Many congrats to Ninon Christol from our Microbial Gene Expression research unit, IBPC CNRS, as well as to @maximiliankohl.bsky.social from IBMC at Univ. Strasbourg, for their amazing poster prizes!
September 4, 2025 at 11:05 AM
Many congrats to Ninon Christol from our Microbial Gene Expression research unit, IBPC CNRS, as well as to @maximiliankohl.bsky.social from IBMC at Univ. Strasbourg, for their amazing poster prizes!
Happy to have presented my work at the #microbialRNAs meeting today, with a very active discussion and a beautiful session! Looking forward to more science in the next few days in Strasbourg.
September 1, 2025 at 7:57 PM
Happy to have presented my work at the #microbialRNAs meeting today, with a very active discussion and a beautiful session! Looking forward to more science in the next few days in Strasbourg.
Reposted by Jonathan Jagodnik
JOB ALERT 🚨 We are hiring TWO principal investigators in cell, molecular, systems, or chemical biology in Toronto, Canada at @sinaihealth.bsky.social. We provide a generous startup, fully funded salary and academic appointment at U of Toronto.
www.nature.com/naturecareer...
Please repost!
www.nature.com/naturecareer...
Please repost!
August 28, 2025 at 6:34 AM
JOB ALERT 🚨 We are hiring TWO principal investigators in cell, molecular, systems, or chemical biology in Toronto, Canada at @sinaihealth.bsky.social. We provide a generous startup, fully funded salary and academic appointment at U of Toronto.
www.nature.com/naturecareer...
Please repost!
www.nature.com/naturecareer...
Please repost!
Reposted by Jonathan Jagodnik
🚨 New Preprint Alert 🚨
Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄
Check it out here: www.biorxiv.org/content/10.1...
Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄
Check it out here: www.biorxiv.org/content/10.1...
August 24, 2025 at 6:38 AM
🚨 New Preprint Alert 🚨
Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄
Check it out here: www.biorxiv.org/content/10.1...
Our latest work, A Zur-dependent regulatory RNA involved in maintaining zinc homeostasis in Staphylococcus aureus, is now live on bioRxiv! 🧬🦠📄
Check it out here: www.biorxiv.org/content/10.1...
Beautiful paper on translation start sites and extented SD motifs in Staph. aureus. www.biorxiv.org/content/10.1...
Congrats to colleagues in Strasburg univ.!
Congrats to colleagues in Strasburg univ.!
Extended Shine-Dalgarno motifs govern translation initiation in Staphylococcus aureus
Regulation of translation initiation is central to bacterial adaptation, but species-specific mechanisms remain poorly understood. We present high-resolution mapping of translation start sites in S. a...
www.biorxiv.org
June 27, 2025 at 1:05 PM
Beautiful paper on translation start sites and extented SD motifs in Staph. aureus. www.biorxiv.org/content/10.1...
Congrats to colleagues in Strasburg univ.!
Congrats to colleagues in Strasburg univ.!
What a fantastic achievement! Carine Tisné is rewarded the CNRS Silver medal for her structural studies of tRNA modification. We are very proud of her, at the Microbial Gene Expression research department, IBPC! www.insb.cnrs.fr/fr/personne/...
Carine Tisné
www.insb.cnrs.fr
June 20, 2025 at 6:52 AM
What a fantastic achievement! Carine Tisné is rewarded the CNRS Silver medal for her structural studies of tRNA modification. We are very proud of her, at the Microbial Gene Expression research department, IBPC! www.insb.cnrs.fr/fr/personne/...