ArticleScientific reports2017
Elucidating the 16S rRNA 3' boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 27 citations in OpenAlex.
- Fitness Effects of Phenotypic Mutations at Proteome-Scale Reveal Optimality of Translation Machinery.Molecular biology and evolution · 2024Article
- Unraveling the plasticity of translation initiation in prokaryotes: Beyond the invariant Shine-Dalgarno sequence.PloS one · 2024Article
- Exploring and Engineering Novel Strong Promoters for High-Level Protein Expression inMicroorganisms · 2023Article
- RNase Y Autoregulates Its Synthesis inMicroorganisms · 2023Article
- Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli.Nucleic acids research · 2023Article
- The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation.RNA biology · 2021Review
- The length of ribosomal binding site spacer sequence controls the production yield for intracellular and secreted proteins by Bacillus subtilis.Microbial cell factories · 2020Article
- Unique Shine-Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation.Genome biology and evolution · 2019Article
- Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis.Poultry science · 2019Article
- RNA-Seq-Based Analysis Reveals Heterogeneity in Mature 16S rRNA 3' Termini and Extended Anti-Shine-Dalgarno Motifs in Bacterial Species.G3 (Bethesda, Md.) · 2018Article
- Re-annotation of 12,495 prokaryotic 16S rRNA 3' ends and analysis of Shine-Dalgarno and anti-Shine-Dalgarno sequences.PloS one · 2018Article
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3 authors at 1 institution in 1 country.
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Abstract
Bacterial translation initiation is influenced by base pairing between the Shine-Dalgarno (SD) sequence in the 5' UTR of mRNA and the anti-SD (aSD) sequence at the free 3' end of the 16S rRNA (3' TAIL) due to: 1) the SD/aSD sequence binding location and 2) SD/aSD binding affinity. In order to understand what makes an SD/aSD interaction optimal, we must define: 1) terminus of the 3' TAIL and 2) extent of the core aSD sequence within the 3' TAIL. Our approach to characterize these components in Escherichia coli and Bacillus subtilis involves 1) mapping the 3' boundary of the mature 16S rRNA using high-throughput RNA sequencing (RNA-Seq), and 2) identifying the segment within the 3' TAIL that is strongly preferred in SD/aSD pairing. Using RNA-Seq data, we resolve previous discrepancies in the reported 3' TAIL in B. subtilis and recovered the established 3' TAIL in E. coli. Furthermore, we extend previous studies to suggest that both highly and lowly expressed genes favor SD sequences with intermediate binding affinity, but this trend is exclusive to SD sequences that complement the core aSD sequences defined herein.
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