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Профиль

Zeynep Baharoglu

Профиль Vively

RNA modifications, antibiotic tolerance, bacterial stress, non coding RNAs, Vibrio cholerae. EPICS lab - Institut Pasteur & EGM (IBPC, CNRS)

journals.asm.org/doi/10.1128/... comprehensive review of bacterial RNA modifications 🦠

Compendium of RNA modifications for bacterial stress adaptation | Microbiology and Molecular Biology ReviewsSUMMARYRNA modifications in the tRNA, rRNA, and mRNA constitute a widespread layer of post-transcriptional gene regulation, commonly known as the epitranscriptome. In bacteria, tRNA and rRNA modifications are well documented and play essential roles in tRNA folding, rRNA maturation, translation, and peptidyl transfer. Although mRNA modifications have been extensively characterized in eukaryotes, their functional implications for mRNA fate in prokaryotes remain uncertain, and their identities and locations are the subject of an emerging field of research. Importantly, RNA modification is a dynamic process, and variation in the presence and abundance of these modifications has significant consequences for bacterial physiology. Here, we discuss current knowledge of modified RNA nucleotides in bacteria, with a particular focus on their roles in bacterial adaptation to environmental stress.journals.asm.org
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Multi-omics analysis identifies a role for Streptococcus suis MnmE in growth regulation and environmental adaptation 🦠 journals.asm.org/doi/10.1128/...

Multi-omics analysis identifies a role for Streptococcus suis MnmE in growth regulation and environmental adaptation | Microbiology SpectrumStreptococcus suis is a major swine and zoonotic pathogen. While bacterial tRNA modifications are known to fine-tune translation, their role in coordinating pathogenesis and stress adaptation remains…journals.asm.org
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AUA codon decoding by preferential use of tRNAIle(UAU) in Lactobacillus casei rnajournal.cshlp.org/content/earl... S4U modif impacts aminoacylation of specific ile isodecoder, t6A impacts recognition 🦠

AUA codon decoding by preferential use of tRNAIle(UAU) in Lactobacillus caseiA monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organismsrnajournal.cshlp.org
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journals.plos.org/plosbiology/... #RNAsky

Queuosine tRNA modification regulates translational adaptation and virulence of Leishmania mexicanaRegulation of gene expression in the protozoan parasite Leishmania mexicana is known to be largely post-transcriptional, but the control of these processes is still not fully understood. This study sh...journals.plos.org
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QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing 💫💫https://academic.oup.com/nargab/article/8/3/lqag065/8725956?login=false

QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencingAbstract. Transfer RNAs (tRNAs) are essential for protein synthesis and are extensively modified to ensure their structure and function. Direct RNA sequencacademic.oup.com
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Widespread immune systems protect bacteria against conjugative plasmids 🦠 www.biorxiv.org/content/10.6...

Widespread immune systems protect bacteria against conjugative plasmidsConjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...www.biorxiv.org
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16S ribosomal RNA modification drives transcript-specific translation efficiency #RNAsky 🦠 RsmH in B. subtilis www.biorxiv.org/content/10.6...

16S ribosomal RNA modification drives transcript-specific translation efficiencyBacterial ribosomal RNAs (rRNAs) are decorated with conserved nucleotide modifications, but the functionality of these modifications is often underexplored. MraW (RsmH) is a 16S rRNA methyltransferase...www.biorxiv.org
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Functional divergence and conservation in the QueC protein family (PF06508): from tRNA modification to anti-phage defense 🦠 portlandpress.com/biochemj/art...

Functional divergence and conservation in the QueC protein family (PF06508): from tRNA modification to anti-phage defenseAbstract. The QueC protein family (PF06508) is best known for its role in the biosynthesis of 7-deazaguanine derivatives, including the tRNA modification queuosine and the DNA base 7-cyano-7-deazaguan...portlandpress.com
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Defective queuosine and i6A/ms2i6A modification of tRNATyr cause frameshifting and protein aggregation #RNAsky in 🦠E. coli and S. pombe academic.oup.com/nar/article/...

Defective queuosine and i6A/ms2i6A modification of tRNATyr cause frameshifting and protein aggregationAbstract. Queuosine (Q) modification at the wobble position (Q34) of tRNAs fine-tunes translational speed but is not essential for viability, leaving its pacademic.oup.com
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rRNA modification circuit, with interdependence of modifs by rsmF, RsmH (RsmI?), RsmE in E. coli 🦠 www.biorxiv.org/content/10.6... 💫 #rnasky

E. coli RsmF activity depends on prior modification of 16S rRNA helix 44Bacterial ribosomal RNA (rRNA) methylations are important for accurate translation. Four distinct methylations incorporated by RsmE, RsmF, and RsmH/ RsmI form a cluster of three modified 16S rRNA nucl...www.biorxiv.org
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Studying the regulons of OmrA and OmrB paralogous small RNAs reveals targets involved in central carbon metabolism and lipogenesis 🦠 www.biorxiv.org/content/10.6... 💫 @egmresearch.bsky.social

Studying the regulons of OmrA and OmrB paralogous small RNAs reveals targets involved in central carbon metabolism and lipogenesisSmall regulatory RNAs (sRNAs) are key players in bacterial adaptation to stress. They often occupy central positions in regulatory networks and control the expression of multiple targets. In a strikin...www.biorxiv.org
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Conservation and evolution of the ribosome across the photosynthetic lineage🦠🍓''gain and loss of ribosomal proteins, rRNA modifications and hibernation factors upon endosymbiosis'' www.biorxiv.org/content/10.6...

Conservation and evolution of the ribosome across the photosynthetic lineageRegulated biogenesis of photosynthetic proteins by the chloroplast ribosomes is central to plant development and environmental adaptation. Here, we describe changes to the ribosome that occurred durin...www.biorxiv.org
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A detailed molecular picture of protein folding during active translation www.biorxiv.org/content/10.6...

A detailed molecular picture of protein folding during active translationAll proteins can begin to fold on the ribosome, and many proteins critically rely on co-translational folding to attain their native conformation. The molecular details underlying this crucial process...www.biorxiv.org
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☀️🔥 New RNA-modification newsletter, heat-wave edition: wobble mods, QueC evolution, tRNA thiolation, host signals rewiring virulence translation, bacterial mRNA fate, and a bonus chapter on ribosome heterogeneity, hibernation & dormancy. 🦠 Stay cool, modify your RNAs.

☀️🔥🏜️ RNA Modifications Newsletter - June-July 2026Issue #12rnamodifupdates.substack.com
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Increased temperature selects for antibiotic resistance genes in a model aquatic ecosystem #AMR 🦠 www.nature.com/articles/s44...

Increased temperature selects for antibiotic resistance genes in a model aquatic ecosystem - npj Antimicrobials and Resistancenpj Antimicrobials and Resistance - Increased temperature selects for antibiotic resistance genes in a model aquatic ecosystemwww.nature.com
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AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis www.biorxiv.org/content/10.6...

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysisTransfer RNA (tRNA) molecules serve as essential adapters during protein translation. While direct RNA sequencing (DRS) via Oxford Nanopore Technologies has emerged as a powerful platform for systemat...www.biorxiv.org
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ModkitOpt: An optimised workflow for RNA modification stoichiometry estimation and site calling from nanopore sequencing www.biorxiv.org/content/10.6...

ModkitOpt: An optimised workflow for RNA modification stoichiometry estimation and site calling from nanopore sequencingDespite enabling single-molecule detection of RNA modifications, nanopore direct RNA sequencing lacks standardised approaches for modification site calling. This requires accurately quantifying per-si...www.biorxiv.org
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Conformational diversity of collided ribosomes determines stress signaling www.biorxiv.org/content/10.6...

Conformational diversity of collided ribosomes determines stress signalingTranslating ribosomes are stalled by amino acid starvation and by chemical damage of the mRNA template, leading to ribosome collisions. These collisions serve as signaling platforms that promote quali...www.biorxiv.org
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A variant rRNA serves as a translational repressor in Plasmodium falciparum www.biorxiv.org/content/10.6...

A variant rRNA serves as a translational repressor in Plasmodium falciparumRibosome composition can vary through differences in associated proteins, post-transcriptional and post-translational modifications. Such heterogeneity enables ribosomes to respond to environmental[1]...www.biorxiv.org
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Mapping biological and chemical dimensions of antimicrobial resistance pollution and exposures due to treated wastewater discharges into US surface waters at the national scale #AMR 🦠 www.sciencedirect.com/science/arti...

www.sciencedirect.com
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