ArticleeLife2019
A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
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Who cites it
139 citing papers in PubMed, 255 citations in OpenAlex.
- Pyrrolysine supply and demand shapes the translational landscape inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols.Nucleic acids research · 2026Article
- Collided ribosomes are rescued by the endonuclease Rae1 andbioRxiv : the preprint server for biology · 2026Article
- Translation factors that keep the ribosome Pro-active.Microbiology and molecular biology reviews : MMBR · 2026Review
- Purification of MNase for Use in Ribosomal Profiling of High-Salinity Extremophiles.Bio-protocol · 2026Article
- Folding the message: mRNA structure as a regulatory layer of human mitochondrial gene expression.Biochimica et biophysica acta. Molecular cell research · 2026Review
- Comprehensive post-transcriptional modification profiles in individual Staphylococcus aureus tRNA species.Nucleic acids research · 2026Article
- The transcriptional and translational outcomes for pseudogenes in bacterial endosymbionts.Molecular biology and evolution · 2026Article
- Article
- Probing the limits of genetic recoding using multi-omics-guided evolution.Nature communications · 2026Article
- A transfer RNA inosine modification drives genome-wide synonymous recoding across human commensal bacterial families.PNAS nexus · 2026Article
- pCODE tRNA Expression Plasmids Compensate for Rare Codons in Recombinant Protein Production.ACS synthetic biology · 2026Article
- iTP-seq: a scalable profiling workflow to characterize bacterial translation landscapes in vitro.Nature protocols · 2026Review
- Translation efficiency covariation identifies conserved coordination patterns across cell types.Nature biotechnology · 2026Article
- 2'-O-Methylation maintains ribosome structural and translation integrity.Molecular cell · 2026Article
- Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs.Nucleic acids research · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- Abridged Ribosome Profiling for Accurate Bacterial Translation Measurements.Methods and protocols · 2026Article
- Structural modification of oxazolidinone antibiotics alters nascent peptide stalling preference and peptide trajectory through the ribosome.bioRxiv : the preprint server for biology · 2026Article
- Extended Shine-Dalgarno motifs govern translation initiation in Staphylococcus aureus.Nature communications · 2026Article
79 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
In eukaryotes, ribosome profiling provides insight into the mechanism of protein synthesis at the codon level. In bacteria, however, the method has been more problematic and no consensus has emerged for how to best prepare profiling samples. Here, we identify the sources of these problems and describe new solutions for arresting translation and harvesting cells in order to overcome them. These improvements remove confounding artifacts and improve the resolution to allow analyses of ribosome behavior at the codon level. With a clearer view of the translational landscape in vivo, we observe that filtering cultures leads to translational pauses at serine and glycine codons through the reduction of tRNA aminoacylation levels. This observation illustrates how bacterial ribosome profiling studies can yield insight into the mechanism of protein synthesis at the codon level and how these mechanisms are regulated in response to changes in the physiology of the cell.
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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.