ArticleMethods in molecular biology (Clifton, N.J.)2021
Identification of Translation Start Sites in Bacterial Genomes.
Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 9 citations in OpenAlex.
- Approaches for Studying Context Specificity of Translation Inhibitor Action.International journal of molecular sciences · 2026Review
- Ribosome Profiling Methods Adapted to the Study of RNA-Dependent Translation Regulation in Staphylococcus aureus.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century.Microbial biotechnology · 2023Review
- INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors.Nucleic acids research · 2022Article
- Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing.Scientific reports · 2022Article
- Phage Annotation Guide: Guidelines for Assembly and High-Quality Annotation.PHAGE (New Rochelle, N.Y.) · 2021Article
- Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria.eLife · 2020Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The knowledge of translation start sites is crucial for annotation of genes in bacterial genomes. However, systematic mapping of start codons in bacterial genes has mainly relied on predictions based on protein conservation and mRNA sequence features which, although useful, are not always accurate. We recently found that the pleuromutilin antibiotic retapamulin (RET) is a specific inhibitor of translation initiation that traps ribosomes specifically at start codons, and we used it in combination with ribosome profiling to map start codons in the Escherichia coli genome. This genome-wide strategy, that was named Ribo-RET, not only verifies the position of start codons in already annotated genes but also enables identification of previously unannotated open reading frames and reveals the presence of internal start sites within genes. Here, we provide a detailed Ribo-RET protocol for E. coli. Ribo-RET can be adapted for mapping the start codons of the protein-coding sequences in a variety of bacterial species.
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Registered trials
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