RNA Processing and Degradation in Bacterial Systems

The life cycle of RNA in bacteria encompasses a finely tuned balance between synthesis, maturation and decay, ensuring that transcripts are available in the right amounts and at the right times. Primary transcripts—including messenger RNAs (mRNAs), transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs)—undergo processing steps such as endonucleolytic cleavage, exonucleolytic trimming and chemical modifications that stabilise structures or earmark molecules for turnover. Translation and decay are often coupled: ribosomes can shield mRNAs from nucleolytic attack, whereas stalled ribosomes or specific sequence elements can trigger targeted degradation. Central to these processes are multienzyme assemblies known as RNA degradosomes, which coordinate RNase activities, RNA helicases and metabolic enzymes and, in many species, localise to the inner cytoplasmic membrane to prevent premature rRNA processing. Recent high-resolution mapping of cleavage sites and structural analyses of RNase–substrate complexes have revealed dynamic regulatory networks that respond to environmental cues, stress and antibiotic exposure. Understanding these pathways informs the design of novel antimicrobial strategies targeting RNase function and enables synthetic biology approaches that harness mRNA stability for precise gene expression control.

Research from Nature Portfolio

Structural studies have resolved intermediates in the degradation of the 30S ribosomal subunit by RNase R, revealing how the enzyme initially engages the platform to remove the anti-Shine–Dalgarno sequence and decoding-site helix, then overcomes a kinetic barrier at the neck region via head-domain rearrangement to complete subunit disassembly. These insights provide a mechanistic framework for ribosome quality control and turnover. Complementing this, a comprehensive atlas of 5′-monophosphorylated mRNA decay intermediates across 96 bacterial species has demonstrated that cotranslational decay is a conserved strategy. By correlating ribosome positions with exonucleolytic and endonucleolytic cleavage patterns, this work has uncovered stress- and drug-induced pausing events at codon resolution and enabled species-specific profiling of post-transcriptional responses in complex microbiomes.

RNA Processing and Degradation in Bacterial Systems publication trend

The graph below shows the total number of articles in rna processing and degradation in bacterial systems across all publications each year (not limited to Nature Index journals).

Technical terms

Endoribonuclease: An enzyme that cleaves RNA at internal phosphodiester bonds, initiating decay or processing.

Exoribonuclease: An enzyme that degrades RNA from the 5′ or 3′ end, trimming nucleotides sequentially.

RNA degradosome: A multienzyme complex coordinating RNA processing, unwinding and degradation in bacteria.

Degradome sequencing: A high-throughput technique for mapping the 5′ ends of RNA decay intermediates genome-wide.

Cotranslational decay: The process by which mRNA is sequentially degraded while still associated with translating ribosomes.

Cryo-EM: A method that images macromolecular complexes at cryogenic temperatures to determine near-atomic structures.

References

1. Structural basis of ribosomal 30S subunit degradation by RNase R. Nature (2024).
2. Atlas of mRNA translation and decay for bacteria. Nature Microbiology (2023).
3. Selective RNA Processing and Stabilization are Multi‐Layer and Stoichiometric Regulators of Gene Expression in Escherichia coli. Advanced Science (2023).
4. Methodologies for bacterial ribonuclease characterization using RNA-seq. FEMS Microbiology Reviews (2023).
5. Attachment of the RNA degradosome to the bacterial inner cytoplasmic membrane prevents wasteful degradation of rRNA in ribosome assembly intermediates. PLOS Biology (2023).