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Compendium of RNA modifications for bacterial stress adaptation | Microbiology and Molecular Biology Reviews

SUMMARYRNA 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

Multi-omics analysis identifies a role for Streptococcus suis MnmE in growth regulation and environmental adaptation | Microbiology Spectrum

Streptococcus 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

AUA codon decoding by preferential use of tRNAIle(UAU) in Lactobacillus casei

A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms

rnajournal.cshlp.org

Queuosine tRNA modification regulates translational adaptation and virulence of Leishmania mexicana

Regulation 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

QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing

Abstract. Transfer RNAs (tRNAs) are essential for protein synthesis and are extensively modified to ensure their structure and function. Direct RNA sequenc

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Widespread immune systems protect bacteria against conjugative plasmids

Conjugative 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...

biorxiv.org

16S ribosomal RNA modification drives transcript-specific translation efficiency

Bacterial 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...

biorxiv.org

Functional divergence and conservation in the QueC protein family (PF06508): from tRNA modification to anti-phage defense

Abstract. 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

Defective queuosine and i6A/ms2i6A modification of tRNATyr cause frameshifting and protein aggregation

Abstract. Queuosine (Q) modification at the wobble position (Q34) of tRNAs fine-tunes translational speed but is not essential for viability, leaving its p

academic.oup.com

E. coli RsmF activity depends on prior modification of 16S rRNA helix 44

Bacterial 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...

biorxiv.org

Studying the regulons of OmrA and OmrB paralogous small RNAs reveals targets involved in central carbon metabolism and lipogenesis

Small 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...

biorxiv.org

Conservation and evolution of the ribosome across the photosynthetic lineage

Regulated 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...

biorxiv.org

A detailed molecular picture of protein folding during active translation

All 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...

biorxiv.org

☀️🔥🏜️ RNA Modifications Newsletter - June-July 2026

Issue #12

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Increased temperature selects for antibiotic resistance genes in a model aquatic ecosystem - npj Antimicrobials and Resistance

npj Antimicrobials and Resistance - Increased temperature selects for antibiotic resistance genes in a model aquatic ecosystem

nature.com

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

Transfer 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...

biorxiv.org

ModkitOpt: An optimised workflow for RNA modification stoichiometry estimation and site calling from nanopore sequencing

Despite enabling single-molecule detection of RNA modifications, nanopore direct RNA sequencing lacks standardised approaches for modification site calling. This requires accurately quantifying per-si...

biorxiv.org

Conformational diversity of collided ribosomes determines stress signaling

Translating 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...

biorxiv.org

A variant rRNA serves as a translational repressor in Plasmodium falciparum

Ribosome composition can vary through differences in associated proteins, post-transcriptional and post-translational modifications. Such heterogeneity enables ribosomes to respond to environmental[1]...

biorxiv.org

sciencedirect.com

Increased temperature selects for antibiotic resistance genes in a model aquatic ecosystem - npj Antimicrobials and Resistance

npj Antimicrobials and Resistance - Increased temperature selects for antibiotic resistance genes in a model aquatic ecosystem

nature.com

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

Transfer 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...

biorxiv.org

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Antibiotics stimulate protein transfer to persister cells

The exchange of biological matter between bacterial cells drives adaptation and evolution. However, whether bacteria can exchange functional proteins remains unclear. In this work, we found that antib...

science.org

Nicotinamide-Based Covalent Inhibitors of tRNA (m1G37) Methyltransferase (TrmD) to Increase Antibacterial Activity

Bacterial tRNA (m1G37) methyltransferase (TrmD) is an essential enzyme required for accurate translation and represents an attractive antibacterial target distinct from its eukaryotic counterpart, Trm...

pubs.acs.org