ArticleNature microbiology2023
Atlas of mRNA translation and decay for bacteria.
Article in Nature microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 27 citations in OpenAlex.
- 5PSeq Explorer: interactive analysis of co-translational mRNA decay and ribosome dynamics.RNA biology · 2026Article
- Regulation of multiple paralogs of a small subunit ribosomal protein inRNA (New York, N.Y.) · 2026Article
- Leaky recombinant expression reveals design constraints of bicistronic synthetic operons in Escherichia coli.Scientific reports · 2026Article
- A streamlined, nanopore-compatible 5PSeq protocol for rapid phenotypic antimicrobial sensitivity testing.Cell reports methods · 2026Article
- Enhanced genetic stability and expression control in growth-decoupled continuous two-stage E. coli fermentations using plasmid-dependent thyA auxotrophic selection.Microbial cell factories · 2025Article
- Rif-seq reveals Caulobacter crescentus mRNA decay is globally coordinated with transcription and translation.Cell reports · 2025Article
- Structure of the 30S translation initiation complex coupled to paused RNA polymerase and its potential for riboregulation.Nature communications · 2025Article
- Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli.Nucleic acids research · 2025Article
- The DnaJK chaperone ofmBio · 2025Article
- Regulation of co-translational mRNA decay by PAP and DXO1 in Arabidopsis.BMC plant biology · 2025Article
- The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans.Scientific reports · 2024Article
- Resolution of ribosomal stalling by EF-P and ABCF ATPases YfmR and YkpA/YbiT.Nucleic acids research · 2024Article
- Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance.Nucleic acids research · 2024Article
- Article
- Epitranscriptional m6A modification of rRNA negatively impacts translation and host colonization in Staphylococcus aureus.PLoS pathogens · 2024Article
- Methodologies for bacterial ribonuclease characterization using RNA-seq.FEMS microbiology reviews · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 6 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Regulation of messenger RNA stability is pivotal for programmed gene expression in bacteria and is achieved by a myriad of molecular mechanisms. By bulk sequencing of 5' monophosphorylated mRNA decay intermediates (5'P), we show that cotranslational mRNA degradation is conserved among both Gram-positive and -negative bacteria. We demonstrate that, in species with 5'-3' exonucleases, the exoribonuclease RNase J tracks the trailing ribosome to produce an in vivo single-nucleotide toeprint of the 5' position of the ribosome. In other species lacking 5'-3' exonucleases, ribosome positioning alters endonucleolytic cleavage sites. Using our metadegradome (5'P degradome) sequencing approach, we characterize 5'P mRNA decay intermediates in 96 species including Bacillus subtilis, Escherichia coli, Synechocystis spp. and Prevotella copri and identify codon- and gene-level ribosome stalling responses to stress and drug treatment. We also apply 5'P sequencing to complex clinical and environmental microbiomes and demonstrate that metadegradome sequencing provides fast, species-specific posttranscriptional characterization of responses to drug or environmental perturbations. Finally we produce a degradome atlas for 96 species to enable analysis of mechanisms of RNA degradation in bacteria. Our work paves the way for the application of metadegradome sequencing to investigation of posttranscriptional regulation in unculturable species and complex microbial communities.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.