Zeynep Baharoglu

Pseudouridine selects RNAs for extracellular transport www.biorxiv.org/content/10.1...

Rifampicin-induced Staphylococcus aureus persister formation is driven by CodY regulon and oxidative stress level 🦠https://www.biorxiv.org/content/10.64898/2026.03.03.709237v1

Interstep compatibility of a model for the prebiotic synthesis of RNA consistent with Hadean natural history | PNAS Models for prebiotic syntheses often have many steps, each separately validated by laboratory experiments. The challenge then asks whether these st...

RNA from scratch.. 💫 Interstep compatibility of a model for the prebiotic synthesis of RNA consistent with Hadean natural history | PNAS
www.pnas.org/doi/10.1073/...

Stress 🧨, bacteria 🦠, Fe-S by @sronneau.bsky.social lab

🧬✏️ 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

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria - Nature Communications The authors investigate the distribution of the aminoglycoside resistance gene npmA in Gram-positive bacteria via a mobile genetic element, highlighting its global presence and cross-species transfer ...

multi resistance dissemination with rRNA modification enzyme on mobile genetic element 🦠 #AMR #RNAbiology #rnasky

A reprogrammed genetic code consisting of 32 distinct amino acids Abstract. Sense codon reassignment enables ribosomal incorporation of nonproteinogenic amino acids (npAAs) at any of the 61 sense codons. Because npAAs rep

doi.org/10.1093/nar/...

Global response to antibiotic exposure reveals a critical role for nucleotide metabolism in high-level β-lactam tolerance - npj Antimicrobials and Resistance npj Antimicrobials and Resistance - Global response to antibiotic exposure reveals a critical role for nucleotide metabolism in high-level β-lactam tolerance

"targeting nucleotide synthesis synergizes with β-lactam-mediated killing in hypertolerant V. cholerae, Klebsiella pneumoniae and E. coli." 🦠

Welcome to bluesky EGM unit 😊🦠 bsky.app/profile/egmr...

Quantitative RNA pseudouridine landscape reveals dynamic modification patterns and evolutionary conservation across bacterial species 🦠https://www.biorxiv.org/content/10.1101/2025.05.13.653745v2.full

Mechanism of 30S subunit recognition and modification by the conserved bacterial ribosomal RNA methyltransferase RsmI 🦠
www.biorxiv.org/content/10.1...

Climate change and antimicrobial resistance - Nature Reviews Microbiology In this work, Kalanxhi and Laxminarayan review the evidence supporting the links between climate change and antimicrobial resistance, highlight opportunities for action and identify areas wherein furt...

On the need for more research into the relationship between climate change and antimicrobial resistance. 🦠 #AMR

Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein Properties of biomolecules; Epigenetics; Microbial genomics; Transcriptomics

Cytosine methylation contributes to the fitness of Caulobacter cells naturally expressing a Vsr-like protein: iScience www.cell.com/iscience/ful... 🦠

Epitranscriptomic control of stress adaptations in Escherichia coli Abstract. The impacts of various stressors on bacterial systems have been studied at the phenotypic, transcriptional, and translational levels during the e

🦠💫 RNA modifications and stress

🧬 RNA Modifications Newsletter – February 2026 ⛸️ issue #8

⛸️🧬 February RNA Modifications Newsletter

From CRISPR-triggered tRNA tail cleavage to temperature-responsive rRNA modifications, ribosome QC, and pathway-specific rRNA modification during biogenesis.
#RNAmods #Epitranscriptomics #Ribosome #Translation #tRNA #rRNA

Cleavage of host tRNAs by mycoplasma membrane-associated nuclease Abstract. Mycoplasmas are pathogens causing infectious diseases in various animals, including humans. They are also common contaminants of cell culture. Al

🦠 #rnasky #rnabiology

Multilayered regulation by RNA thermometers enables precise control of Cas9 expression in E. coli Abstract. Cas9-based genome editing technologies can rapidly generate mutations to probe a diverse array of mutant genotypes. However, aberrant Cas9 nuclea

🦠

TlyA is a 23S and 16S 2′-O-methylcytidine methyltransferase important for ribosome assembly in Bacillus subtilis Abstract. Ribosomal RNA (rRNA) methylation is conserved across biology, yet the effect of rRNA methylation on ribosome function is poorly understood. In th

accumulation of the 50S subunit in delta-tlyA with cold sensitive phenotype and resistance to aminoglycosides 🦠 #RNAmodifications #RNAbiology #rnasky

Synonymous codon usage defines functional gene families - BMC Biology Background The degeneracy of the genetic code is increasingly recognized for roles in regulating translation rate, protein folding, and cell response. However, the functional genomics of codon usage p...

Signature codon usage patterns define functional gene families, this is in yeast and could be also very informative for bacteria and link with tRNA modifs #rnasky #codonusage #rnabiology #rnamodifications

trans-Translation inhibitors that kill M. tuberculosis and pathogenic Non-tuberculous Mycobacteria have a dual mechanism of action www.biorxiv.org/content/10.6...

Ψ-Atlas: An Integrated Atlas for Pseudouridine Epitranscriptome Abstract. Pseudouridine (Ψ) is a C5 glycoside isomer of uridine, formed by breaking the N1 glycosyl bond and undergoing a 180° base rotation. This modifica

academic.oup.com/gpb/advance-...

Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation - Nature Communications Small regulatory RNAs can act on target mRNAs to control their translation and stability. Here, the authors present evidence that this riboregulation can potentially regulate by pairing to a target si...

Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation #rnasky 🦠

Probing the epitranscriptome and RNA damage with nanopore direct RNA sequencing #tnasky

AlphaFold protein interaction modeling tutorial and workshop - the Node This video is the culmination of several years attempting to: (1) Figure out best practices for modeling protein-protein interactions; (2) Understand the This video is the culmination of several years...

'This video is the culmination of several yrs attempting to: (1) Figure out best practices for modeling ptn-ptn interactions; (2) Understand the outputs of programs like AlphaFold & adjacent software including quantitative metrics;(3) Communicate my thoughts to unwitting victims through workshops'

Redox-driven ADAR1 activation promotes Okazaki fragment maturation and DNA replication integrity - Nature Structural & Molecular Biology Chen et al. show that redox signals activate ADAR1 to fix faulty RNA pieces during DNA copying, ensuring smooth replication and protecting genome stability.

A to I RNA editing at the replication fork #RNAsky #RNAbiology

Carboxymethylcytosine is a natural base modification and a handle for bacteriophage DNA hypermodification - Nature Communications DNA in many bacteriophages contains unusual chemical modifications. Here, the authors discover that carboxymethylcytosine is a natural DNA base and reveal its role as an intermediate enabling further ...

DNA modif and phages 🦠

The DinG exonuclease acts as a primary quality controller to remove unprocessed ribosomal RNAs Abstract. Bacteria lacking DEAD-box RNA-helicases often show reduced growth and aberrant maturation of ribosomal subunits resulting in fewer active ribosom

#RNAsky #RNAbiology #ribosome 🦠

Help without a comic about your research for the greater good!
#microsky #science #virosky #ecoevo

Stress-Induced Cooperation Promotes Tolerance in Resource-Limited Auxotrophic Microbial Consortia Microbial communities often rely on metabolic cooperation, especially under nutrient limitation, but how antibiotics influence these interactions remains unclear. Here, we show that exposure to chlora...

"under low amino acid availability, co-cultures of leucine and phenylalanine auxotrophs display greater tolerance to chloramphenicol than monocultures"=> community level tolerance 🦠

Mechanistic insights into E. coli recovery from growth arrest Bacteria survive hostile conditions in clinically relevant conditions by shutting down protein synthesis, but how they restart growth remains poorly understood. Here, we use an E. coli delta-rimM stra...

Role of RimM ribosome maturation factor in recovery after protein synthesis arrest 🦠 #ribosome #rnasky #rnabiology